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mmodel

inetrpolation

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Dear List –

Does anyone know of a software (preferably an ImageJ plug-in) that would fill areas generated by a mask to make them merge smoothly with the surrounding areas?

For instance, a control image may be taken to identify artefacts. The question is, then, how to remove small unwanted objects from the main image without creating unsightly holes. Something like automatic “healing brush” in Photoshop.

Michael Model, Ph.D.

Confocal Microscopy Core

Dpt. Biological Sciences

Kent State University

Kent, OH 44242

tel. 330-672-2874

Chris Tully

Re: inetrpolation

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Michael,

Depending on the relative sizes of the artifacts and the objects of interest, there are two common approaches to this problem. For very small noise artifacts (1 to ~9 pixels in area) the Process|Noise|Despeckle filter is the best choice. Despeckle is a 3x3 Median filter; and is the best choice since it does not affect the edges of larger objects. It functions by evaluating each 3x3 neighborhood in the image and replacing the center pixel with the median value of the nine pixels in the neighborhood. For objects larger than 3x3 but still significantly smaller than the objects of interest, the Process|Binary|Open and Process|Binary|Close filters are useful, since although they do affect edges (smooth) they do leave the edges of larger objects in almost exactly same location that they started.

Chris Tully

--
Chris Tully
Microscopy and Image Analysis Expert
[hidden email]
240-888-1021
http://www.linkedin.com/in/christully

On Thu, May 8, 2008 at 10:09 AM, MODEL, MICHAEL <[hidden email]> wrote:

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Dear List –

Does anyone know of a software (preferably an ImageJ plug-in) that would fill areas generated by a mask to make them merge smoothly with the surrounding areas?

For instance, a control image may be taken to identify artefacts. The question is, then, how to remove small unwanted objects from the main image without creating unsightly holes. Something like automatic "healing brush" in Photoshop.

Michael Model, Ph.D.

Confocal Microscopy Core

Dpt. Biological Sciences

Kent State University

Kent, OH 44242

tel. 330-672-2874

mmodel

Re: interpolation

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Thanks Chris. But doesn’t opening/closing work only on binary images?

From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Chris Tully
Sent: Thursday, May 08, 2008 10:56 AM
To: [hidden email]
Subject: Re: inetrpolation

On Thu, May 8, 2008 at 10:09 AM, MODEL, MICHAEL <[hidden email]> wrote:

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Dear List –

Does anyone know of a software (preferably an ImageJ plug-in) that would fill areas generated by a mask to make them merge smoothly with the surrounding areas?

Michael Model, Ph.D.

Confocal Microscopy Core

Dpt. Biological Sciences

Kent State University

Kent, OH 44242

tel. 330-672-2874

Glen MacDonald-2

Re: inetrpolation

In reply to this post by mmodel

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

What about a gaussian filter applied to the mask or your flatfield
image?

Glen
Glen MacDonald
Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
Box 357923
University of Washington
Seattle, WA 98195-7923 USA
(206) 616-4156
[hidden email]

************************************************************************
******
The box said "Requires WindowsXP or better", so I bought a Macintosh.
************************************************************************
******

On May 8, 2008, at 7:09 AM, MODEL, MICHAEL wrote:

> Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-
> bin/wa?S1=confocal
> Dear List –
>
> Does anyone know of a software (preferably an ImageJ plug-in) that
> would fill areas generated by a mask to make them merge smoothly
> with the surrounding areas?
> For instance, a control image may be taken to identify artefacts.
> The question is, then, how to remove small unwanted objects from
> the main image without creating unsightly holes. Something like
> automatic “healing brush” in Photoshop.
>
> Michael Model, Ph.D.
> Confocal Microscopy Core
> Dpt. Biological Sciences
> Kent State University
> Kent, OH 44242
> tel. 330-672-2874
>

Chris Tully

Re: interpolation

In reply to this post by mmodel

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Michael,

Unfortunately, you are correct about the behavior of the Open and Close filters in Image J. I discovered that shortly after posting my comment. I have far more experience with Image-Pro Plus (http://www.mediacy.com), where all of the filters can operate on any class of image. With that aside, it may still be useful to create a mask of your initial pass at finding objects, filter it with the Open or Close filter and then use the filtered mask to restrict object finding on the original image.

Chris

--
Chris Tully
Microscopy and Image Analysis Expert
[hidden email]
240-888-1021
http://www.linkedin.com/in/christully

On Thu, May 8, 2008 at 11:17 AM, MODEL, MICHAEL <[hidden email]> wrote:

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Thanks Chris. But doesn't opening/closing work only on binary images?

From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Chris Tully
Sent: Thursday, May 08, 2008 10:56 AM
To: [hidden email]
Subject: Re: inetrpolation

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Michael,

Depending on the relative sizes of the artifacts and the objects of interest, there are two common approaches to this problem. For very small noise artifacts (1 to ~9 pixels in area) the Process|Noise|Despeckle filter is the best choice. Despeckle is a 3x3 Median filter; and is the best choice since it does not affect the edges of larger objects. It functions by evaluating each 3x3 neighborhood in the image and replacing the center pixel with the median value of the nine pixels in the neighborhood. For objects larger than 3x3 but still significantly smaller than the objects of interest, the Process|Binary|Open and Process|Binary|Close filters are useful, since although they do affect edges (smooth) they do leave the edges of larger objects in almost exactly same location that they started.

Chris Tully

--
Chris Tully
Microscopy and Image Analysis Expert
[hidden email]
240-888-1021
http://www.linkedin.com/in/christully

On Thu, May 8, 2008 at 10:09 AM, MODEL, MICHAEL <[hidden email]> wrote:

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Dear List –

Does anyone know of a software (preferably an ImageJ plug-in) that would fill areas generated by a mask to make them merge smoothly with the surrounding areas?

For instance, a control image may be taken to identify artefacts. The question is, then, how to remove small unwanted objects from the main image without creating unsightly holes. Something like automatic "healing brush" in Photoshop.

Michael Model, Ph.D.

Confocal Microscopy Core

Dpt. Biological Sciences

Kent State University

Kent, OH 44242

tel. 330-672-2874

Jeremy Adler

Re: interpolation Note of Caution

In reply to this post by mmodel

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Removal of artefacts.

1) Smooth your artefact free image, and use the mask to select the areas from the smoothed image that you wish to insert into the original. Only fiddle the problematic pixels. This will only work for small artefacts.

However it is worth asking why you wish wish to 'improve' the appearance of your images and whether this is ethical.
At the very least a full description of why and how the published image differs from the original image must be given.
From your description you appear able to decide that some features are artefacts and define these features sufficiently well to accurately generate a mask. If we assume that the artefects simply obliterate any underlying signal then you have no knowledge of what might have been found in those pixels. And no legitimate basis for 'improving' your image.

Zapping the artefacts and leaving clear and obvious blanks would be more legitimate than 'improving' the original, but I would strongly favour publishing the originals and explaining/highlighting the artefacts.
Better yet deal with the source of the artefacts.

Jeremy Adler
Cell Biology
The Wenner-Gren Inst.
Arrhenius Laboratories E5
Stockholm University
Stockholm 106 91
Sweden

________________________________

From: Confocal Microscopy List on behalf of MODEL, MICHAEL
Sent: Thu 5/8/2008 16:09
To: [hidden email]
Subject: inetrpolation

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Dear List -

Does anyone know of a software (preferably an ImageJ plug-in) that would fill areas generated by a mask to make them merge smoothly with the surrounding areas?

For instance, a control image may be taken to identify artefacts. The question is, then, how to remove small unwanted objects from the main image without creating unsightly holes. Something like automatic "healing brush" in Photoshop.

Michael Model, Ph.D.

Confocal Microscopy Core

Dpt. Biological Sciences

Kent State University

Kent, OH 44242

tel. 330-672-2874

Zoltan

Re: interpolation Note of Caution

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

I'm completely with Jeremy on this subject, I don't think it's good practice to remove parts of your image just for its own sake. You can e.g. false-colour the real or the artificial pixels, in order to show the readers which objects to pay attention to. Just my 2c of course.

Zoltan

On Fri, May 9, 2008 at 8:37 AM, Jeremy Adler <[hidden email]> wrote:

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Removal of artefacts.

1) Smooth your artefact free image, and use the mask to select the areas from the smoothed image that you wish to insert into the original. Only fiddle the problematic pixels. This will only work for small artefacts.

However it is worth asking why you wish wish to 'improve' the appearance of your images and whether this is ethical.
At the very least a full description of why and how the published image differs from the original image must be given.
From your description you appear able to decide that some features are artefacts and define these features sufficiently well to accurately generate a mask. If we assume that the artefects simply obliterate any underlying signal then you have no knowledge of what might have been found in those pixels. And no legitimate basis for 'improving' your image.

Zapping the artefacts and leaving clear and obvious blanks would be more legitimate than 'improving' the original, but I would strongly favour publishing the originals and explaining/highlighting the artefacts.
Better yet deal with the source of the artefacts.

Jeremy Adler
Cell Biology
The Wenner-Gren Inst.
Arrhenius Laboratories E5
Stockholm University
Stockholm 106 91
Sweden

________________________________

From: Confocal Microscopy List on behalf of MODEL, MICHAEL
Sent: Thu 5/8/2008 16:09
To: [hidden email]
Subject: inetrpolation

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Dear List -

Does anyone know of a software (preferably an ImageJ plug-in) that would fill areas generated by a mask to make them merge smoothly with the surrounding areas?

For instance, a control image may be taken to identify artefacts. The question is, then, how to remove small unwanted objects from the main image without creating unsightly holes. Something like automatic "healing brush" in Photoshop.

Michael Model, Ph.D.

Confocal Microscopy Core

Dpt. Biological Sciences

Kent State University

Kent, OH 44242

tel. 330-672-2874

--
--
Zoltan Cseresnyes
Facility manager, Imaging Suite
Dept. of Zoology University of Cambridge

RICHARD BURRY

Re: interpolation Note of Caution

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

There are ethical limits as to what is allowed in manipulating micrographs. Removing small unwanted objects is no different than adding small wanted objects. A great summary with examples is found in a Journal of Cell Biology article by Rossner and Yamada 2004 166:11-15 with the pdf available at http://www.jcb.org/cgi/reprint/166/1/11. Journal editors are looking for these modifications because authors are misrepresentating their data!

Dick Burry
Ohio State University

----- Original Message -----
From: Zoltan Cseresnyes <[hidden email]>
Date: Friday, May 9, 2008 8:33 am
Subject: Re: interpolation Note of Caution
To: [hidden email]

> Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

> On Fri, May 9, 2008 at 8:37 AM, Jeremy Adler <<A href="javascript:main.compose('new','t=adler.jeremy@cellbio.su.se')">adler.jeremy@...> wrote:

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

> Removal of artefacts.

> 1) Smooth your artefact free image, and use the mask to select the areas from the smoothed image that you wish to insert into the original. Only fiddle the problematic pixels. This will only work for small artefacts.

> However it is worth asking why you wish wish to 'improve' the appearance of your images and whether this is ethical.
> At the very least a full description of why and how the published image differs from the original image must be given.
> From your description you appear able to decide that some features are artefacts and define these features sufficiently well to accurately generate a mask. If we assume that the artefects simply obliterate any underlying signal then you have no knowledge of what might have been found in those pixels. And no legitimate basis for 'improving' your image.

> Zapping the artefacts and leaving clear and obvious blanks would be more legitimate than 'improving' the original, but I would strongly favour publishing the originals and explaining/highlighting the artefacts.
> Better yet deal with the source of the artefacts.

> Jeremy Adler
> Cell Biology
> The Wenner-Gren Inst.
> Arrhenius Laboratories E5
> Stockholm University
> Stockholm 106 91
> Sweden

> ________________________________

> From: Confocal Microscopy List on behalf of MODEL, MICHAEL
> Sent: Thu 5/8/2008 16:09
> To: <A href="javascript:main.compose('new','t=CONFOCAL@LISTSERV.BUFFALO.EDU')">CONFOCAL@...
> Subject: inetrpolation

> Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

> Dear List -

> Does anyone know of a software (preferably an ImageJ plug-in) that would fill areas generated by a mask to make them merge smoothly with the surrounding areas?

> For instance, a control image may be taken to identify artefacts. The question is, then, how to remove small unwanted objects from the main image without creating unsightly holes. Something like automatic "healing brush" in Photoshop.

> Michael Model, Ph.D.

> Confocal Microscopy Core

> Dpt. Biological Sciences

> Kent State University

> Kent, OH 44242

> tel. 330-672-2874

> --
> --
> Zoltan Cseresnyes
> Facility manager, Imaging Suite
> Dept. of Zoology University of Cambridge

> Spam
> Not spam
> Forget previous vote

Richard W. Burry, Ph.D.
Department of Neuroscience, College of Medicine
Campus Microscopy and Imaging Facility, Director
The Ohio State University
Associate Editor, Journal of Histochemistry and Cytochemistry
3018 Graves Hall
333 West Tenth Avenue
Columbus, Ohio 43210
Voice 614.292.2814 Cell 614.638.3345 Fax 614.688.8742

Eric Scarfone

Re: interpolation Note of Caution

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Hello all
this problem certainly deserves a whole thread (it probably has been
on this list before?).
I wonder how one should consider techniques such as background
subtraction that have been in use in video-microscopy even before the
digital age!
Isn't it also manipulation?
Eric

Eric Scarfone, PhD, CNRS,
Center for Hearing and communication Research
Department of Clinical Neuroscience
Karolinska Institutet

Postal Address:
CFH, M1:02
Karolinska Hospital,
SE-171 76 Stockholm, Sweden

Work: +46 (0)8-517 79343,
Cell: +46 (0)70 888 2352
Fax: +46 (0)8-301876

email: [hidden email]
http://www.ki.se/cfh/

----- Original Message -----
From: RICHARD BURRY <[hidden email]>
Date: Friday, May 9, 2008 3:28 pm
Subject: Re: interpolation Note of Caution
To: [hidden email]

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
There are ethical limits as to what is allowed in
manipulating micrographs. 
Removing small unwanted objects is no different than adding
small wanted objects.  A
great summary with examples is found in a Journal of Cell Biology
article by Rossner and Yamada 2004 166:11-15 with the pdf available at
http://www.jcb.org/cgi/reprint/166/1/11.  Journal editors are looking for these modifications
because authors are misrepresentating their data!<?xml:namespace
prefix = o ns = "urn:schemas-microsoft-
com:office:office" /><o:p></o:p>
Dick Burry Ohio State University -----
Original Message ----- From: Zoltan Cseresnyes
<[hidden email]> Date: Friday, May 9, 2008 8:33
am Subject: Re: interpolation Note of Caution To:
[hidden email] >
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal I'm
completely with Jeremy on this subject, I don't think it's good
practice to remove parts of your image just for its own
sake.  You can e.g. false-colour the real or the artificial
pixels, in order to show the readers which objects to pay attention
to.  Just my 2c of course.   > Zoltan 
<DIV class=gmail_quote>> On
Fri, May 9, 2008 at 8:37 AM, Jeremy Adler <<A
href="java_script:main.compose('new','t=[hidden email]')"
target="1">[hidden email]</A>> wrote: 
<BLOCKQUOTE class=gmail_quote style="PADDING-LEFT: 1ex; MARGIN: 0px
0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">> Search the CONFOCAL archive at <A
href="http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal"
target=1>>
http://listserv.acsu.buffalo.edu/cgi-bin/wa?
S1=confocal</A> >
Removal of artefacts. >
1) Smooth your artefact free image, and use the mask to select
the areas from the smoothed image that you wish to insert into the
original. Only fiddle the problematic pixels. This will only work for
small artefacts. 
>      However it
is worth asking why you wish wish to 'improve' the appearance of your
images and whether this is ethical. >     At the very least a full
description of why and how the published image differs from the
original image must be given. >
    From your description you appear able to decide
that some features are artefacts and define these features
sufficiently well to accurately generate a mask.  If we assume
that the artefects simply obliterate any underlying signal then you
have no knowledge of what might have been found in those pixels. And
no legitimate basis for 'improving' your image. <FO
NT style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;
BACKGROUND-COLOR: #f5f8f0">>    Zapping the
artefacts and leaving clear and obvious blanks would be more
legitimate than 'improving' the original, but I would strongly favour
publishing the originals and explaining/highlighting the
artefacts. > Better yet deal
with the source of the artefacts. > Jeremy Adler >
Cell Biology > The
Wenner-Gren Inst. >
Arrhenius Laboratories E5 >
Stockholm University >
Stockholm 106 91 >
Sweden >
________________________________ > From: Confocal Microscopy List on behalf of
MODEL, MICHAEL > Sent: Thu
5/8/2008 16:09 > To: <A href="java_script:main.compose
('new','t=[hidden email]')"
target="1">[hidden email]</A> > Subject: inetrpolation > Search the CONFOCAL archive at
<A href="http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal"
target=1>http://listserv.acsu.buffalo.edu/cgi-bin/wa?
S1=confocal</A> > Dear
List - > Does
anyone know of a software (preferably an ImageJ plug-in) that would
fill areas generated by a mask to make them merge smoothly with the
surrounding areas? > For instance, a control image may be taken
to identify artefacts. The question is, then, how to remove small
unwanted objects from the main image without creating unsightly holes.
Something like automatic "healing brush" in
Photoshop. >
Michael Model, Ph.D. >
Confocal Microscopy Core > Dpt. Biological Sciences > Kent State University > Kent, OH 44242 > tel. 330-672-
2874 </BLOCKQUOTE> > -- > -- >
Zoltan Cseresnyes >
Facility manager, Imaging Suite >  Dept. of Zoology University of
Cambridge 
<HR>
 <A href="https://antispam.osu.edu/b.php?
c=s&i=597223478&m=473bf06adf8d" target=1>> Spam</A> <A
href="https://antispam.osu.edu/b.php?
c=n&i=597223478&m=473bf06adf8d" target=1>> Not spam</A> <A
href="https://antispam.osu.edu/b.php?
c=f&i=597223478&m=473bf06adf8d" target=1>> Forget previous vote</A>  Richard W. Burry, Ph.D.
 Department of Neuroscience, College of Medicine Campus
Microscopy and Imaging Facility, Director The Ohio State
University Associate Editor, Journal of Histochemistry and
Cytochemistry 3018 Graves Hall 333 West Tenth Avenue Col
umbus, Ohio 43210 Voice 614.292.2814  Cell 614.638.3345 
Fax 614.688.8742 </DIV>

mmodel

Re: interpolation Note of Caution

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

I certainly didn't' expect to start a big discussion of this topic. I
agree that the Notes of Caution are fully justified. On the other hand,
in Russ' Image Processing Handbook you will find many examples of very
drastic editing of microscopic images, so in some situations it must be
acceptable. Is it up to each journal to set up their own guidelines? It
seems to me that so long as the author fully explained what had been
done to the images it's not cheating, but I may be wrong. (I think we
already had this discussion on this forum before).

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On
Behalf Of Eric Scarfone
Sent: Friday, May 09, 2008 9:46 AM
To: [hidden email]
Subject: Re: interpolation Note of Caution

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Hello all
this problem certainly deserves a whole thread (it probably has been
on this list before?).
I wonder how one should consider techniques such as background
subtraction that have been in use in video-microscopy even before the
digital age!
Isn't it also manipulation?
Eric

Eric Scarfone, PhD, CNRS,
Center for Hearing and communication Research
Department of Clinical Neuroscience
Karolinska Institutet

Postal Address:
CFH, M1:02
Karolinska Hospital,
SE-171 76 Stockholm, Sweden

Work: +46 (0)8-517 79343,
Cell: +46 (0)70 888 2352
Fax: +46 (0)8-301876

email: [hidden email]
http://www.ki.se/cfh/

----- Original Message -----
From: RICHARD BURRY <[hidden email]>
Date: Friday, May 9, 2008 3:28 pm
Subject: Re: interpolation Note of Caution
To: [hidden email]

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
There are ethical limits as to what is allowed in
manipulating micrographs. 
Removing small unwanted objects is no different than adding
small wanted objects.  A
great summary with examples is found in a Journal of Cell Biology
article by Rossner and Yamada 2004 166:11-15 with the pdf available at
http://www.jcb.org/cgi/reprint/166/1/11.  Journal editors are looking for these modifications
because authors are misrepresentating their data!<?xml:namespace
prefix = o ns = "urn:schemas-microsoft-
com:office:office" /><o:p></o:p>
Dick Burry Ohio State University -----
Original Message ----- From: Zoltan Cseresnyes
<[hidden email]> Date: Friday, May 9, 2008 8:33
am Subject: Re: interpolation Note of Caution To:
[hidden email] >
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal I'm
completely with Jeremy on this subject, I don't think it's good
practice to remove parts of your image just for its own
sake.  You can e.g. false-colour the real or the artificial
pixels, in order to show the readers which objects to pay attention
to.  Just my 2c of course.   > Zoltan 
<DIV class=gmail_quote>> On
Fri, May 9, 2008 at 8:37 AM, Jeremy Adler <<A
href="java_script:main.compose('new','t=[hidden email]')"
target="1">[hidden email]</A>> wrote: 
<BLOCKQUOTE class=gmail_quote style="PADDING-LEFT: 1ex; MARGIN: 0px
0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">> Search the CONFOCAL archive at <A
href="http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal"
target=1>>
http://listserv.acsu.buffalo.edu/cgi-bin/wa?
S1=confocal</A> >
Removal of artefacts. >
1) Smooth your artefact free image, and use the mask to select
the areas from the smoothed image that you wish to insert into the
original. Only fiddle the problematic pixels. This will only work for
small artefacts. 
>      However it
is worth asking why you wish wish to 'improve' the appearance of your
images and whether this is ethical. >     At the very least a full
description of why and how the published image differs from the
original image must be given. >
    From your description you appear able to decide
that some features are artefacts and define these features
sufficiently well to accurately generate a mask.  If we assume
that the artefects simply obliterate any underlying signal then you
have no knowledge of what might have been found in those pixels. And
no legitimate basis for 'improving' your image. <FO
NT style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;
BACKGROUND-COLOR: #f5f8f0">>    Zapping the
artefacts and leaving clear and obvious blanks would be more
legitimate than 'improving' the original, but I would strongly favour
publishing the originals and explaining/highlighting the
artefacts. > Better yet deal
with the source of the artefacts. > Jeremy Adler >
Cell Biology > The
Wenner-Gren Inst. >
Arrhenius Laboratories E5 >
Stockholm University >
Stockholm 106 91 >
Sweden >
________________________________ > From: Confocal Microscopy List on behalf of
MODEL, MICHAEL > Sent: Thu
5/8/2008 16:09 > To: <A href="java_script:main.compose
('new','t=[hidden email]')"
target="1">[hidden email]</A> > Subject: inetrpolation > Search the CONFOCAL archive at
<A href="http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal"
target=1>http://listserv.acsu.buffalo.edu/cgi-bin/wa?
S1=confocal</A> > Dear
List - > Does
anyone know of a software (preferably an ImageJ plug-in) that would
fill areas generated by a mask to make them merge smoothly with the
surrounding areas? > For instance, a control image may be taken
to identify artefacts. The question is, then, how to remove small
unwanted objects from the main image without creating unsightly holes.
Something like automatic "healing brush" in
Photoshop. >
Michael Model, Ph.D. >
Confocal Microscopy Core > Dpt. Biological Sciences > Kent State University > Kent, OH 44242 > tel. 330-672-
2874 </BLOCKQUOTE> > -- > -- >
Zoltan Cseresnyes >
Facility manager, Imaging Suite >  Dept. of Zoology University of
Cambridge 
<HR>
 <A href="https://antispam.osu.edu/b.php?
c=s&i=597223478&m=473bf06adf8d" target=1>> Spam</A> <A
href="https://antispam.osu.edu/b.php?
c=n&i=597223478&m=473bf06adf8d" target=1>> Not spam</A> <A
href="https://antispam.osu.edu/b.php?
c=f&i=597223478&m=473bf06adf8d" target=1>> Forget previous vote</A>  Richard W. Burry, Ph.D.
 Department of Neuroscience, College of Medicine Campus
Microscopy and Imaging Facility, Director The Ohio State
University Associate Editor, Journal of Histochemistry and
Cytochemistry 3018 Graves Hall 333 West Tenth Avenue Col
umbus, Ohio 43210 Voice 614.292.2814  Cell 614.638.3345 
Fax 614.688.8742 </DIV>

cromey

Re: interpolation Note of Caution

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

I've been thinking about the issue of digital imaging ethics for awhile.
Much of what we could get away with in the days of the photographic darkroom
would no longer be considered appropriate these days. The JCB has pretty
explicit digital image guidelines, I suspect that other journals that are
without specific guidelines are probably "behind the curve".

My take has always been that if you fully describe the steps that are taken
in processing an image, then no one can accuse you of misconduct (1).
Reviewers & Editors may not like your image processing protocol, but then it
becomes an issue of scientific discussion, not an accusation.

I've proposed some digital imaging ethical guidelines here:
http://swehsc.pharmacy.arizona.edu/exppath/micro/digimage_ethics.html

Some colleagues at the University of Alabama - Birmingham are working on a
web site that includes these guidelines and a video case study, but it's not
quite done yet. I'll post the URL when the folks at UAB let me know they
are done.

Doug Cromey

(1) The HHS Office of Research Integrity officially defines scientific
misconduct as: ".fabrication, falsification, or plagiarism in proposing,
performing, or reviewing research, or in reporting research results."

* Fabrication is making up data or results and recording or reporting them.
* Falsification is manipulating research materials, equipment, or processes,
or changing or omitting data or results such that the research is not
accurately represented in the research record.
* Plagiarism is the appropriation of another person's ideas, processes,
results, or words without giving appropriate credit.
* Research misconduct does not include differences of opinion.

FROM: http://ori.hhs.gov/publications/ori_intro_text.shtml

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Douglas W. Cromey, M.S. - Assistant Scientific Investigator
Dept. of Cell Biology & Anatomy, University of Arizona
1501 N. Campbell Ave, Tucson, AZ 85724-5044 USA

office: AHSC 4212 email: [hidden email]
voice: 520-626-2824 fax: 520-626-2097

http://swehsc.pharmacy.arizona.edu/exppath/
Home of: "Microscopy and Imaging Resources on the WWW"

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On
Behalf Of MODEL, MICHAEL
Sent: Friday, May 09, 2008 7:43 AM
To: [hidden email]
Subject: Re: interpolation Note of Caution

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

I certainly didn't' expect to start a big discussion of this topic. I
agree that the Notes of Caution are fully justified. On the other hand,
in Russ' Image Processing Handbook you will find many examples of very
drastic editing of microscopic images, so in some situations it must be
acceptable. Is it up to each journal to set up their own guidelines? It
seems to me that so long as the author fully explained what had been
done to the images it's not cheating, but I may be wrong. (I think we
already had this discussion on this forum before).

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On
Behalf Of Eric Scarfone
Sent: Friday, May 09, 2008 9:46 AM
To: [hidden email]
Subject: Re: interpolation Note of Caution

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Hello all
this problem certainly deserves a whole thread (it probably has been
on this list before?).
I wonder how one should consider techniques such as background
subtraction that have been in use in video-microscopy even before the
digital age!
Isn't it also manipulation?
Eric

Eric Scarfone, PhD, CNRS,
Center for Hearing and communication Research
Department of Clinical Neuroscience
Karolinska Institutet

Postal Address:
CFH, M1:02
Karolinska Hospital,
SE-171 76 Stockholm, Sweden

Work: +46 (0)8-517 79343,
Cell: +46 (0)70 888 2352
Fax: +46 (0)8-301876

email: [hidden email]
http://www.ki.se/cfh/

----- Original Message -----
From: RICHARD BURRY <[hidden email]>
Date: Friday, May 9, 2008 3:28 pm
Subject: Re: interpolation Note of Caution
To: [hidden email]

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
There are ethical limits as to what is allowed in
manipulating micrographs. 
Removing small unwanted objects is no different than adding
small wanted objects.  A
great summary with examples is found in a Journal of Cell Biology
article by Rossner and Yamada 2004 166:11-15 with the pdf available at
http://www.jcb.org/cgi/reprint/166/1/11.  Journal editors are looking for these modifications
because authors are misrepresentating their data!<?xml:namespace
prefix = o ns = "urn:schemas-microsoft-
com:office:office" /><o:p></o:p>
Dick Burry Ohio State University -----
Original Message ----- From: Zoltan Cseresnyes
<[hidden email]> Date: Friday, May 9, 2008 8:33
am Subject: Re: interpolation Note of Caution To:
[hidden email] >
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal I'm
completely with Jeremy on this subject, I don't think it's good
practice to remove parts of your image just for its own
sake.  You can e.g. false-colour the real or the artificial
pixels, in order to show the readers which objects to pay attention
to.  Just my 2c of course.   > Zoltan 
<DIV class=gmail_quote>> On
Fri, May 9, 2008 at 8:37 AM, Jeremy Adler <<A
href="java_script:main.compose('new','t=[hidden email]')"
target="1">[hidden email]</A>> wrote: 
<BLOCKQUOTE class=gmail_quote style="PADDING-LEFT: 1ex; MARGIN: 0px
0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">> Search the CONFOCAL archive at <A
href="http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal"
target=1>>
http://listserv.acsu.buffalo.edu/cgi-bin/wa?
S1=confocal</A> >
Removal of artefacts. >
1) Smooth your artefact free image, and use the mask to select
the areas from the smoothed image that you wish to insert into the
original. Only fiddle the problematic pixels. This will only work for
small artefacts. 
>      However it
is worth asking why you wish wish to 'improve' the appearance of your
images and whether this is ethical. >     At the very least a full
description of why and how the published image differs from the
original image must be given. >
    From your description you appear able to decide
that some features are artefacts and define these features
sufficiently well to accurately generate a mask.  If we assume
that the artefects simply obliterate any underlying signal then you
have no knowledge of what might have been found in those pixels. And
no legitimate basis for 'improving' your image. <FO
NT style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;
BACKGROUND-COLOR: #f5f8f0">>    Zapping the
artefacts and leaving clear and obvious blanks would be more
legitimate than 'improving' the original, but I would strongly favour
publishing the originals and explaining/highlighting the
artefacts. > Better yet deal
with the source of the artefacts. > Jeremy Adler >
Cell Biology > The
Wenner-Gren Inst. >
Arrhenius Laboratories E5 >
Stockholm University >
Stockholm 106 91 >
Sweden >
________________________________ > From: Confocal Microscopy List on behalf of
MODEL, MICHAEL > Sent: Thu
5/8/2008 16:09 > To: <A href="java_script:main.compose
('new','t=[hidden email]')"
target="1">[hidden email]</A> > Subject: inetrpolation > Search the CONFOCAL archive at
<A href="http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal"
target=1>http://listserv.acsu.buffalo.edu/cgi-bin/wa?
S1=confocal</A> > Dear
List - > Does
anyone know of a software (preferably an ImageJ plug-in) that would
fill areas generated by a mask to make them merge smoothly with the
surrounding areas? > For instance, a control image may be taken
to identify artefacts. The question is, then, how to remove small
unwanted objects from the main image without creating unsightly holes.
Something like automatic "healing brush" in
Photoshop. >
Michael Model, Ph.D. >
Confocal Microscopy Core > Dpt. Biological Sciences > Kent State University > Kent, OH 44242 > tel. 330-672-
2874 </BLOCKQUOTE> > -- > -- >
Zoltan Cseresnyes >
Facility manager, Imaging Suite >  Dept. of Zoology University of
Cambridge 
<HR>
 <A href="https://antispam.osu.edu/b.php?
c=s&i=597223478&m=473bf06adf8d" target=1>> Spam</A> <A
href="https://antispam.osu.edu/b.php?
c=n&i=597223478&m=473bf06adf8d" target=1>> Not spam</A> <A
href="https://antispam.osu.edu/b.php?
c=f&i=597223478&m=473bf06adf8d" target=1>> Forget previous vote</A>  Richard W. Burry, Ph.D.
 Department of Neuroscience, College of Medicine Campus
Microscopy and Imaging Facility, Director The Ohio State
University Associate Editor, Journal of Histochemistry and
Cytochemistry 3018 Graves Hall 333 West Tenth Avenue Col
umbus, Ohio 43210 Voice 614.292.2814  Cell 614.638.3345 
Fax 614.688.8742 </DIV>

RICHARD BURRY

Re: interpolation Note of Caution

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

The guidelines Doug posted on the Univ. Arizona website are great. One issue that makes digital images more suspect, is the individual element of the image, the pixel, can be changed. With photographic manipulations we were burning in regions not selectively changing the intensity of a single pixel. Most journals today reserve the right to ask authors for the original image files that were taken on the CCD camera or came from the confocal. As listed by Doug in his guidelines, it is most important to retain archive files of ALL original images. This allows you to go back to the original if needed.

One mistake that authors are making in submitted manuscripts is to saturate the intense pixels in images. The images look almost like line drawings and not micrographs. It is important to keep all the information in the images when processing and to adjust the settings when collecting images to spread the intensity over the full range.

Dick Burry
Ohio State University

----- Original Message -----
From: Doug Cromey <[hidden email]>
Date: Monday, May 12, 2008 12:54 pm
Subject: Re: interpolation Note of Caution
To: [hidden email]

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> I've been thinking about the issue of digital imaging ethics for
> awhile.Much of what we could get away with in the days of the
> photographic darkroom
> would no longer be considered appropriate these days. The
> JCB has pretty
> explicit digital image guidelines, I suspect that other journals
> that are
> without specific guidelines are probably "behind the
> curve".
>
> My take has always been that if you fully describe the steps
> that are taken
> in processing an image, then no one can accuse you of misconduct (1).
> Reviewers & Editors may not like your image processing protocol,
> but then it
> becomes an issue of scientific discussion, not an accusation.
>
> I've proposed some digital imaging ethical guidelines here:
> http://swehsc.pharmacy.arizona.edu/exppath/micro/digimage_ethics.html
>
> Some colleagues at the University of Alabama - Birmingham are
> working on a
> web site that includes these guidelines and a video case study,
> but it's not
> quite done yet. I'll post the URL when the folks at UAB
> let me know they
> are done.
>
> Doug Cromey
>
>
> (1) The HHS Office of Research Integrity officially defines scientific
> misconduct as: ".fabrication, falsification, or plagiarism
> in proposing,
> performing, or reviewing research, or in reporting research results."
>
> * Fabrication is making up data or results and recording or
> reporting them.
> * Falsification is manipulating research materials, equipment,
> or processes,
> or changing or omitting data or results such that the research
> is not
> accurately represented in the research record.
> * Plagiarism is the appropriation of another person's ideas,
> processes,results, or words without giving appropriate credit.
> * Research misconduct does not include differences of opinion.
>
> FROM: http://ori.hhs.gov/publications/ori_intro_text.shtml
>
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> Douglas W. Cromey, M.S. - Assistant Scientific Investigator
> Dept. of Cell Biology & Anatomy, University of Arizona
> 1501 N. Campbell Ave, Tucson, AZ 85724-5044 USA
>
> office: AHSC
> 4212 email:
> [hidden email]: 520-626-
> 2824 fax: 520-626-2097
>
> http://swehsc.pharmacy.arizona.edu/exppath/
> Home of: "Microscopy and Imaging Resources on the WWW"
>
>
> -----Original Message-----
> From: Confocal Microscopy List
> [mailto:[hidden email]] On
> Behalf Of MODEL, MICHAEL
> Sent: Friday, May 09, 2008 7:43 AM
> To: [hidden email]
> Subject: Re: interpolation Note of Caution
>
> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> I certainly didn't' expect to start a big discussion of this
> topic. I
> agree that the Notes of Caution are fully justified. On the
> other hand,
> in Russ' Image Processing Handbook you will find many examples
> of very
> drastic editing of microscopic images, so in some situations it
> must be
> acceptable. Is it up to each journal to set up their own
> guidelines? It
> seems to me that so long as the author fully explained what had been
> done to the images it's not cheating, but I may be wrong. (I
> think we
> already had this discussion on this forum before).
>
> -----Original Message-----
> From: Confocal Microscopy List
> [mailto:[hidden email]] On
> Behalf Of Eric Scarfone
> Sent: Friday, May 09, 2008 9:46 AM
> To: [hidden email]
> Subject: Re: interpolation Note of Caution
>
> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> Hello all
> this problem certainly deserves a whole thread (it probably has
> been
> on this list before?).
> I wonder how one should consider techniques such as background
> subtraction that have been in use in video-microscopy even
> before the
> digital age!
> Isn't it also manipulation?
> Eric
>
> Eric Scarfone, PhD, CNRS,
> Center for Hearing and communication Research
> Department of Clinical Neuroscience
> Karolinska Institutet
>
> Postal Address:
> CFH, M1:02
> Karolinska Hospital,
> SE-171 76 Stockholm, Sweden
>
> Work: +46 (0)8-517 79343,
> Cell: +46 (0)70 888 2352
> Fax: +46 (0)8-301876
>
> email: [hidden email]
> http://www.ki.se/cfh/
>
>
> ----- Original Message -----
> From: RICHARD BURRY <[hidden email]>
> Date: Friday, May 9, 2008 3:28 pm
> Subject: Re: interpolation Note of Caution
> To: [hidden email]
>
> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
> face="Times New
> Roman">There are ethical limits as to what is
> allowed in
> manipulating micrographs. yes">
> Removing small unwanted objects is no different than
> adding
> small wanted objects.
> A
> great summary with examples is found in a Journal of Cell
> Biology
> article by Rossner and Yamada 2004 166:11-15 with the pdf
> available at
> http://www.jcb.org/cgi/reprint/166/1/11. spacerun:
> yes"> Journal editors are looking for these
> modifications
> because authors are misrepresentating their
> data!<?xml:namespace
> prefix = o ns = "urn:schemas-microsoft-
> com:office:office" /><o:p></o:p>
> Dick Burry Ohio State
> University -----
> Original Message ----- From: Zoltan Cseresnyes
> <[hidden email]> Date: Friday, May 9, 2008 8:33
> am Subject: Re: interpolation Note of Caution To:
> [hidden email] WEIGHT: normal;
> FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> #f5f8f0">>
> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
> I'm
> completely with Jeremy on this subject, I don't think
> it's good
> practice to remove parts of your image just for its own
> sake. You can e.g. false-colour the real or the artificial
> pixels, in order to show the readers which objects to pay
> attention
> to. Just my 2c of course. style="FONT-WEIGHT:
> normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> #f5f8f0">> Zoltan 
> <DIV class=gmail_quote> FONT-SIZE:
> 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> On
> Fri, May 9, 2008 at 8:37 AM, Jeremy Adler <<A
> href="java_script:main.compose('new','t=[hidden email]')"
> target="1">[hidden email]</A>> wrote: 
> <BLOCKQUOTE class=gmail_quote style="PADDING-LEFT: 1ex;
> MARGIN: 0px
> 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"> WEIGHT:
> normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> #f5f8f0">> Search the CONFOCAL archive
> at <A
> href="http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal"
> target=1> FONT-
> STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?
> S1=confocal</A> normal; FONT-SIZE:
> 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> Removal of artefacts. style="FONT-WEIGHT: normal;
> FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> #f5f8f0">>
> 1) Smooth your artefact free image, and use the mask
> to select
> the areas from the smoothed image that you wish to insert into
> the
> original. Only fiddle the problematic pixels. This will only
> work for
> small artefacts. 
> STYLE: normal;
> BACKGROUND-COLOR: #f5f8f0">> 
> However it
> is worth asking why you wish wish to 'improve' the appearance of
> your
> images and whether this is ethical. WEIGHT:
> normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> #f5f8f0">> At the very least a full
> description of why and how the published image differs from the
> original image must be given. normal;
> FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> #f5f8f0">>
> From your description you appear able to
> decide
> that some features are artefacts and define these features
> sufficiently well to accurately generate a mask. If we
> assume
> that the artefects simply obliterate any underlying signal then
> you
> have no knowledge of what might have been found in those pixels.
> And
> no legitimate basis for 'improving' your image. <FO
> NT style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE:
> normal;
> BACKGROUND-COLOR: #f5f8f0">> Zapping
> the
> artefacts and leaving clear and obvious blanks would be more
> legitimate than 'improving' the original, but I would strongly
> favour
> publishing the originals and explaining/highlighting the
> artefacts. 14px; FONT-
> STYLE: normal; BACKGROUND-COLOR: #f5f8f0">> Better
> yet deal
> with the source of the artefacts. style="FONT-WEIGHT:
> normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> #f5f8f0">> Jeremy Adler WEIGHT: normal;
> FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> #f5f8f0">>
> Cell Biology normal; FONT-SIZE:
> 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> The
> Wenner-Gren Inst. FONT-SIZE:
> 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> Arrhenius Laboratories E5 style="FONT-WEIGHT: normal;
> FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> #f5f8f0">>
> Stockholm University WEIGHT: normal; FONT-
> SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> Stockholm 106 91 normal; FONT-
> SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> Sweden normal; FONT-SIZE:
> 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> ________________________________ style="FONT-
> WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-
> COLOR:
> #f5f8f0">> From: Confocal Microscopy List on behalf
> of
> MODEL, MICHAEL SIZE: 14px;
> FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> Sent: Thu
> 5/8/2008 16:09 SIZE: 14px;
> FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">> </
> FONT>To: <A href="java_script:main.compose
> ('new','t=[hidden email]')"
> target="1">[hidden email]</A> style="FONT-
> WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-
> COLOR:
> #f5f8f0">> Subject:
> inetrpolation style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;
> BACKGROUND-COLOR: #f5f8f0">> Search the CONFOCAL
> archive at
> <A href="http://listserv.acsu.buffalo.edu/cgi-
> bin/wa?S1=confocal"
> target=1>http://listserv.acsu.buffalo.edu/cgi-bin/wa?
> S1=confocal</A> normal; FONT-SIZE:
> 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> Dear
> List - normal; FONT-SIZE:
> 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> Does
> anyone know of a software (preferably an ImageJ plug-in) that
> would
> fill areas generated by a mask to make them merge smoothly with
> the
> surrounding areas? T-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;
> BACKGROUND-
> COLOR: #f5f8f0">> For instance, a control image may
> be taken
> to identify artefacts. The question is, then, how to remove
> small
> unwanted objects from the main image without creating unsightly
> holes.
> Something like automatic "healing brush" in
> Photoshop. WEIGHT: normal; FONT-SIZE:
> 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> Michael Model, Ph.D. WEIGHT: normal;
> FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> #f5f8f0">>
> Confocal Microscopy Core style="FONT-WEIGHT:
> normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> #f5f8f0">> Dpt. Biological
> Sciences WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-
> COLOR:
> #f5f8f0">> Kent State
> University WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COL
> OR: #f5f8f0">> Kent, OH 44242 style="FONT-
> WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-
> COLOR:
> #f5f8f0">> tel. 330-672-
> 2874 </BLOCKQUOTE> clear=all> style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;
> BACKGROUND-COLOR: #f5f8f0">> -- style="FONT-
> WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-
> COLOR:
> #f5f8f0">> -- normal; FONT-
> SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> Zoltan Cseresnyes normal; FONT-
> SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> Facility manager, Imaging Suite style="FONT-WEIGHT:
> normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> #f5f8f0">> Dept. of Zoology University of
>
>
> --
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Richard W. Burry, Ph.D.
Department of Neuroscience, College of Medicine
Campus Microscopy and Imaging Facility, Director
The Ohio State University
Associate Editor, Journal of Histochemistry and Cytochemistry
3018 Graves Hall
333 West Tenth Avenue
Columbus, Ohio 43210
Voice 614.292.2814 Cell 614.638.3345 Fax 614.688.8742

Chris Tully

Re: interpolation Note of Caution

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal List members,

First let me explain that although I am no longer associated with them, I have previously worked for Media Cybernetics.

One extremely valuable set of features in Image-Pro Plus (www.mediacy.com) is the Audit Trail and Image or File Signature. The Audit Trail logs every action taken on every open image. This allows you to document exactly what was done with or to the image. The Image and File Signatures are 32 bit check sums that are automatically recorded in the Audit trail at relevant times (Acquisition, save, load...), and are sensitive enough to detect a change of +/- one gray level in one pixel! Paired with the Capture module's Auto Save function, it is possible to:

1) Document that a published image is unchanged. You will need to carefully track such things as cropping to demonstrate this completely, but this is entirely possible.

2) If the image has been altered use successive image signatures (before and after each alteration) to demonstrate that the logged alterations are the only ones that have occurred. If you are going to do this I would recommend saving the image with a new name immediately before any such alteration so that you can demonstrate the alteration again if challenged.

Another approach that I often use is to work on a duplicate of the original image. Change away as much as I need to to do the desired analysis. As the last step of my analysis though I generate outlines of the objects that I am measuring and place them back on the unaltered original image. This both allows me to make some measurements that can only be made on the original image and to demonstrate that the identified objects are still relevant to the original image and therefore to the sample.

Chris

--
Chris Tully
Microscopy and Image Analysis Expert
[hidden email]
240-888-1021
http://www.linkedin.com/in/christully

On Mon, May 12, 2008 at 3:35 PM, RICHARD BURRY <[hidden email]> wrote:

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
The guidelines Doug posted on the Univ. Arizona website are great. One issue that makes digital images more suspect, is the individual element of the image, the pixel, can be changed. With photographic manipulations we were burning in regions not selectively changing the intensity of a single pixel. Most journals today reserve the right to ask authors for the original image files that were taken on the CCD camera or came from the confocal. As listed by Doug in his guidelines, it is most important to retain archive files of ALL original images. This allows you to go back to the original if needed.

One mistake that authors are making in submitted manuscripts is to saturate the intense pixels in images. The images look almost like line drawings and not micrographs. It is important to keep all the information in the images when processing and to adjust the settings when collecting images to spread the intensity over the full range.

Dick Burry
Ohio State University

----- Original Message -----
From: Doug Cromey <[hidden email]>
Date: Monday, May 12, 2008 12:54 pm
Subject: Re: interpolation Note of Caution
To: [hidden email]

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> I've been thinking about the issue of digital imaging ethics for
> awhile.Much of what we could get away with in the days of the
> photographic darkroom
> would no longer be considered appropriate these days. The
> JCB has pretty
> explicit digital image guidelines, I suspect that other journals
> that are
> without specific guidelines are probably "behind the
> curve".
>
> My take has always been that if you fully describe the steps
> that are taken
> in processing an image, then no one can accuse you of misconduct (1).
> Reviewers & Editors may not like your image processing protocol,
> but then it
> becomes an issue of scientific discussion, not an accusation.
>
> I've proposed some digital imaging ethical guidelines here:
> http://swehsc.pharmacy.arizona.edu/exppath/micro/digimage_ethics.html
>
> Some colleagues at the University of Alabama - Birmingham are
> working on a
> web site that includes these guidelines and a video case study,
> but it's not
> quite done yet. I'll post the URL when the folks at UAB
> let me know they
> are done.
>
> Doug Cromey
>
>
> (1) The HHS Office of Research Integrity officially defines scientific
> misconduct as: ".fabrication, falsification, or plagiarism
> in proposing,
> performing, or reviewing research, or in reporting research results."
>
> * Fabrication is making up data or results and recording or
> reporting them.
> * Falsification is manipulating research materials, equipment,
> or processes,
> or changing or omitting data or results such that the research
> is not
> accurately represented in the research record.
> * Plagiarism is the appropriation of another person's ideas,
> processes,results, or words without giving appropriate credit.
> * Research misconduct does not include differences of opinion.
>
> FROM: http://ori.hhs.gov/publications/ori_intro_text.shtml
>
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> Douglas W. Cromey, M.S. - Assistant Scientific Investigator
> Dept. of Cell Biology & Anatomy, University of Arizona
> 1501 N. Campbell Ave, Tucson, AZ 85724-5044 USA
>
> office: AHSC
> 4212 email:
> [hidden email]: 520-626-

> 2824 fax: 520-626-2097
>
> http://swehsc.pharmacy.arizona.edu/exppath/
> Home of: "Microscopy and Imaging Resources on the WWW"
>
>
> -----Original Message-----
> From: Confocal Microscopy List
> [mailto:[hidden email]] On
> Behalf Of MODEL, MICHAEL
> Sent: Friday, May 09, 2008 7:43 AM
> To: [hidden email]
> Subject: Re: interpolation Note of Caution
>
> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> I certainly didn't' expect to start a big discussion of this
> topic. I
> agree that the Notes of Caution are fully justified. On the
> other hand,
> in Russ' Image Processing Handbook you will find many examples
> of very
> drastic editing of microscopic images, so in some situations it
> must be
> acceptable. Is it up to each journal to set up their own
> guidelines? It
> seems to me that so long as the author fully explained what had been
> done to the images it's not cheating, but I may be wrong. (I
> think we
> already had this discussion on this forum before).
>
> -----Original Message-----
> From: Confocal Microscopy List
> [mailto:[hidden email]] On
> Behalf Of Eric Scarfone
> Sent: Friday, May 09, 2008 9:46 AM
> To: [hidden email]
> Subject: Re: interpolation Note of Caution
>
> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> Hello all
> this problem certainly deserves a whole thread (it probably has
> been
> on this list before?).
> I wonder how one should consider techniques such as background
> subtraction that have been in use in video-microscopy even
> before the
> digital age!
> Isn't it also manipulation?
> Eric
>
> Eric Scarfone, PhD, CNRS,
> Center for Hearing and communication Research
> Department of Clinical Neuroscience
> Karolinska Institutet
>
> Postal Address:
> CFH, M1:02
> Karolinska Hospital,
> SE-171 76 Stockholm, Sweden
>
> Work: +46 (0)8-517 79343,
> Cell: +46 (0)70 888 2352
> Fax: +46 (0)8-301876
>
> email: [hidden email]
> http://www.ki.se/cfh/
>
>
> ----- Original Message -----
> From: RICHARD BURRY <[hidden email]>
> Date: Friday, May 9, 2008 3:28 pm
> Subject: Re: interpolation Note of Caution
> To: [hidden email]
>
> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
> face="Times New
> Roman">There are ethical limits as to what is
> allowed in
> manipulating micrographs. yes">
> Removing small unwanted objects is no different than
> adding
> small wanted objects.

> A
> great summary with examples is found in a Journal of Cell
> Biology
> article by Rossner and Yamada 2004 166:11-15 with the pdf
> available at
> http://www.jcb.org/cgi/reprint/166/1/11. spacerun:
> yes"> Journal editors are looking for these

> modifications
> because authors are misrepresentating their
> data!<?xml:namespace
> prefix = o ns = "urn:schemas-microsoft-
> com:office:office" /><o:p></o:p>
> Dick Burry Ohio State
> University -----
> Original Message ----- From: Zoltan Cseresnyes
> <[hidden email]> Date: Friday, May 9, 2008 8:33

> am Subject: Re: interpolation Note of Caution To:
> [hidden email] WEIGHT: normal;
> FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> #f5f8f0">>
> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
> I'm
> completely with Jeremy on this subject, I don't think
> it's good
> practice to remove parts of your image just for its own
> sake. You can e.g. false-colour the real or the artificial

> pixels, in order to show the readers which objects to pay
> attention
> to. Just my 2c of course. style="FONT-WEIGHT:
> normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> #f5f8f0">> Zoltan 

> <DIV class=gmail_quote> FONT-SIZE:
> 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> On
> Fri, May 9, 2008 at 8:37 AM, Jeremy Adler <<A
> href="java_script:main.compose('new','t=[hidden email]')"

> target="1">[hidden email]</A>> wrote: 

> <BLOCKQUOTE class=gmail_quote style="PADDING-LEFT: 1ex;
> MARGIN: 0px
> 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"> WEIGHT:
> normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> #f5f8f0">> Search the CONFOCAL archive

> at <A
> href="http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal"
> target=1> FONT-
> STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?
> S1=confocal</A> normal; FONT-SIZE:
> 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> Removal of artefacts. style="FONT-WEIGHT: normal;
> FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> #f5f8f0">>
> 1) Smooth your artefact free image, and use the mask
> to select
> the areas from the smoothed image that you wish to insert into
> the
> original. Only fiddle the problematic pixels. This will only
> work for
> small artefacts. 
> STYLE: normal;
> BACKGROUND-COLOR: #f5f8f0">> 
> However it
> is worth asking why you wish wish to 'improve' the appearance of
> your
> images and whether this is ethical. WEIGHT:
> normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> #f5f8f0">> At the very least a full

> description of why and how the published image differs from the
> original image must be given. normal;
> FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> #f5f8f0">>
> From your description you appear able to
> decide
> that some features are artefacts and define these features
> sufficiently well to accurately generate a mask. If we

> assume
> that the artefects simply obliterate any underlying signal then
> you
> have no knowledge of what might have been found in those pixels.
> And
> no legitimate basis for 'improving' your image. <FO
> NT style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE:
> normal;
> BACKGROUND-COLOR: #f5f8f0">> Zapping
> the
> artefacts and leaving clear and obvious blanks would be more
> legitimate than 'improving' the original, but I would strongly
> favour
> publishing the originals and explaining/highlighting the
> artefacts. 14px; FONT-
> STYLE: normal; BACKGROUND-COLOR: #f5f8f0">> Better
> yet deal
> with the source of the artefacts. style="FONT-WEIGHT:
> normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> #f5f8f0">> Jeremy Adler WEIGHT: normal;
> FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> #f5f8f0">>
> Cell Biology normal; FONT-SIZE:
> 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> The
> Wenner-Gren Inst. FONT-SIZE:
> 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> Arrhenius Laboratories E5 style="FONT-WEIGHT: normal;
> FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> #f5f8f0">>

> Stockholm University WEIGHT: normal; FONT-
> SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> Stockholm 106 91 normal; FONT-
> SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> Sweden normal; FONT-SIZE:
> 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> ________________________________ style="FONT-
> WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-
> COLOR:
> #f5f8f0">> From: Confocal Microscopy List on behalf
> of
> MODEL, MICHAEL SIZE: 14px;
> FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> Sent: Thu
> 5/8/2008 16:09 SIZE: 14px;
> FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">> </

> FONT>To: <A href="java_script:main.compose
> ('new','t=[hidden email]')"
> target="1">[hidden email]</A> style="FONT-
> WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-
> COLOR:
> #f5f8f0">> Subject:
> inetrpolation style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;
> BACKGROUND-COLOR: #f5f8f0">> Search the CONFOCAL
> archive at
> <A href="http://listserv.acsu.buffalo.edu/cgi-
> bin/wa?S1=confocal"
> target=1>http://listserv.acsu.buffalo.edu/cgi-bin/wa?
> S1=confocal</A> normal; FONT-SIZE:
> 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> Dear
> List - normal; FONT-SIZE:
> 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> Does
> anyone know of a software (preferably an ImageJ plug-in) that
> would
> fill areas generated by a mask to make them merge smoothly with
> the
> surrounding areas? T-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;
> BACKGROUND-
> COLOR: #f5f8f0">> For instance, a control image may
> be taken
> to identify artefacts. The question is, then, how to remove
> small
> unwanted objects from the main image without creating unsightly
> holes.
> Something like automatic "healing brush" in
> Photoshop. WEIGHT: normal; FONT-SIZE:
> 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> Michael Model, Ph.D. WEIGHT: normal;
> FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> #f5f8f0">>
> Confocal Microscopy Core style="FONT-WEIGHT:
> normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> #f5f8f0">> Dpt. Biological
> Sciences WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-
> COLOR:
> #f5f8f0">> Kent State
> University WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COL
> OR: #f5f8f0">> Kent, OH 44242 style="FONT-
> WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-
> COLOR:
> #f5f8f0">> tel. 330-672-

> 2874 </BLOCKQUOTE> clear=all> style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;
> BACKGROUND-COLOR: #f5f8f0">> -- style="FONT-
> WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-
> COLOR:
> #f5f8f0">> -- normal; FONT-
> SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> Zoltan Cseresnyes normal; FONT-
> SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> Facility manager, Imaging Suite style="FONT-WEIGHT:
> normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> #f5f8f0">> Dept. of Zoology University of
>
>
> --
> BEGIN-ANTISPAM-VOTING-LINKS
> ------------------------------------------------------
>
> Teach CanIt if this mail (ID 598043969) is spam:
> Spam:
> https://antispam.osu.edu/b.php?c=s&i=598043969&m=454cda2ec162Not
> spam: https://antispam.osu.edu/b.php?c=n&i=598043969&m=454cda2ec162
> Forget vote:
> https://antispam.osu.edu/b.php?c=f&i=598043969&m=454cda2ec162----
> --------------------------------------------------
> END-ANTISPAM-VOTING-LINKS

>

Richard W. Burry, Ph.D.
Department of Neuroscience, College of Medicine

Campus Microscopy and Imaging Facility, Director
The Ohio State University
Associate Editor, Journal of Histochemistry and Cytochemistry

3018 Graves Hall
333 West Tenth Avenue
Columbus, Ohio 43210
Voice 614.292.2814 Cell 614.638.3345 Fax 614.688.8742

Eric Scarfone

old Biorad format

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Hello all
I vaguely recall a small program that would cut out the infamous
original biorad format (MRC600, 2 channels side by side on the same
image) into one two file stacks (one for each channel). Or was it a
patch in Imaris or another software?
If this exists can somebody point it out?
Amicalement
Erics

Eric Scarfone, PhD, CNRS,
Center for Hearing and communication Research
Department of Clinical Neuroscience
Karolinska Institutet

Postal Address:
CFH, M1:02
Karolinska Hospital,
SE-171 76 Stockholm, Sweden

Work: +46 (0)8-517 79343,
Cell: +46 (0)70 888 2352
Fax: +46 (0)8-301876

email: [hidden email]
http://www.ki.se/cfh/

----- Original Message -----
From: Chris Tully <[hidden email]>
Date: Tuesday, May 13, 2008 0:57 am
Subject: Re: interpolation Note of Caution
To: [hidden email]

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> List members,
>
> First let me explain that although I am no longer associated with
> them, I
> have previously worked for Media Cybernetics.
>
> One extremely valuable set of features in Image-Pro Plus
> (www.mediacy.com)is the Audit Trail and Image or File Signature.
> The Audit Trail logs every
> action taken on every open image. This allows you to document
> exactly what
> was done with or to the image. The Image and File Signatures are
> 32 bit
> check sums that are automatically recorded in the Audit trail at
> relevanttimes (Acquisition, save, load...), and are sensitive
> enough to detect a
> change of +/- one gray level in one pixel! Paired with the
> Capture module's
> Auto Save function, it is possible to:
>
> 1) Document that a published image is unchanged. You will need to
> carefullytrack such things as cropping to demonstrate this
> completely, but this is
> entirely possible.
>
> 2) If the image has been altered use successive image signatures
> (before and
> after each alteration) to demonstrate that the logged alterations
> are the
> only ones that have occurred. If you are going to do this I would
> recommendsaving the image with a new name immediately before any
> such alteration so
> that you can demonstrate the alteration again if challenged.
>
> Another approach that I often use is to work on a duplicate of the
> originalimage. Change away as much as I need to to do the desired
> analysis. As the
> last step of my analysis though I generate outlines of the objects
> that I am
> measuring and place them back on the unaltered original image.
> This both
> allows me to make some measurements that can only be made on the
> originalimage and to demonstrate that the identified objects are
> still relevant to
> the original image and therefore to the sample.
>
> Chris
>
> --
> Chris Tully
> Microscopy and Image Analysis Expert
> [hidden email]
> 240-888-1021
> http://www.linkedin.com/in/christully
>
>
> On Mon, May 12, 2008 at 3:35 PM, RICHARD BURRY <[hidden email]>
> wrote:
> > Search the CONFOCAL archive at
> > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
> >
> > The guidelines Doug posted on the Univ. Arizona website are
> great. One
> > issue that makes digital images more suspect, is the individual
> element of
> > the image, the pixel, can be changed. With photographic
> manipulations we
> > were burning in regions not selectively changing the intensity
> of a single
> > pixel. Most journals today reserve the right to ask authors for

the

> > original image files that were taken on the CCD camera or came
> from the
> > confocal. As listed by Doug in his guidelines, it is most
> important to
> > retain archive files of ALL original images. This allows you to
> go back to
> > the original if needed.
> >
> > One mistake that authors are making in submitted manuscripts is to
> > saturate the intense pixels in images. The images look almost
> like line
> > drawings and not micrographs. It is important to keep all the
> information> in the images when processing and to adjust the
> settings when collecting
> > images to spread the intensity over the full range.
> >
> > Dick Burry
> > Ohio State University
> >
> >
> > ----- Original Message -----
> > From: Doug Cromey <[hidden email]>
> > Date: Monday, May 12, 2008 12:54 pm
> > Subject: Re: interpolation Note of Caution
> > To: [hidden email]
> >
> > > Search the CONFOCAL archive at
> > > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
> > >
> > > I've been thinking about the issue of digital imaging ethics for
> > > awhile.Much of what we could get away with in the days of the
> > > photographic darkroom
> > > would no longer be considered appropriate these days. The
> > > JCB has pretty
> > > explicit digital image guidelines, I suspect that other journals
> > > that are
> > > without specific guidelines are probably "behind the
> > > curve".
> > >
> > > My take has always been that if you fully describe the steps
> > > that are taken
> > > in processing an image, then no one can accuse you of
> misconduct (1).
> > > Reviewers & Editors may not like your image processing protocol,
> > > but then it
> > > becomes an issue of scientific discussion, not an accusation.
> > >
> > > I've proposed some digital imaging ethical guidelines here:
> > >
>

http://swehsc.pharmacy.arizona.edu/exppath/micro/digimage_ethics.html>

>
> > > Some colleagues at the University of Alabama - Birmingham are
> > > working on a
> > > web site that includes these guidelines and a video case study,
> > > but it's not
> > > quite done yet. I'll post the URL when the folks at UAB
> > > let me know they
> > > are done.
> > >
> > > Doug Cromey
> > >
> > >
> > > (1) The HHS Office of Research Integrity officially defines
> scientific> > misconduct as: ".fabrication, falsification, or
> plagiarism> > in proposing,
> > > performing, or reviewing research, or in reporting research
> results."> >
> > > * Fabrication is making up data or results and recording or
> > > reporting them.
> > > * Falsification is manipulating research materials, equipment,
> > > or processes,
> > > or changing or omitting data or results such that the research
> > > is not
> > > accurately represented in the research record.
> > > * Plagiarism is the appropriation of another person's ideas,
> > > processes,results, or words without giving appropriate credit.
> > > * Research misconduct does not include differences of opinion.
> > >
> > > FROM: http://ori.hhs.gov/publications/ori_intro_text.shtml
> > >
> > > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> > > Douglas W. Cromey, M.S. - Assistant Scientific Investigator
> > > Dept. of Cell Biology & Anatomy, University of Arizona
> > > 1501 N. Campbell Ave, Tucson, AZ 85724-5044 USA
> > >
> > > office: AHSC
> > > 4212 email:
> > > [hidden email]: 520-626-
> >
> > > 2824 fax: 520-626-2097
> > >
> > > http://swehsc.pharmacy.arizona.edu/exppath/
> > > Home of: "Microscopy and Imaging Resources on the WWW"
> > >
> > >
> > > -----Original Message-----
> > > From: Confocal Microscopy List
> > > [mailto:[hidden email]] On
> > > Behalf Of MODEL, MICHAEL
> > > Sent: Friday, May 09, 2008 7:43 AM
> > > To: [hidden email]
> > > Subject: Re: interpolation Note of Caution
> > >
> > > Search the CONFOCAL archive at
> > > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
> > >
> > > I certainly didn't' expect to start a big discussion of this
> > > topic. I
> > > agree that the Notes of Caution are fully justified. On the
> > > other hand,
> > > in Russ' Image Processing Handbook you will find many examples
> > > of very
> > > drastic editing of microscopic images, so in some situations it
> > > must be
> > > acceptable. Is it up to each journal to set up their own
> > > guidelines? It
> > > seems to me that so long as the author fully explained what
> had been
> > > done to the images it's not cheating, but I may be wrong. (I
> > > think we
> > > already had this discussion on this forum before).
> > >
> > > -----Original Message-----
> > > From: Confocal Microscopy List
> > > [mailto:[hidden email]] On
> > > Behalf Of Eric Scarfone
> > > Sent: Friday, May 09, 2008 9:46 AM
> > > To: [hidden email]
> > > Subject: Re: interpolation Note of Caution
> > >
> > > Search the CONFOCAL archive at
> > > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
> > >
> > > Hello all
> > > this problem certainly deserves a whole thread (it probably has
> > > been
> > > on this list before?).
> > > I wonder how one should consider techniques such as background
> > > subtraction that have been in use in video-microscopy even
> > > before the
> > > digital age!
> > > Isn't it also manipulation?
> > > Eric
> > >
> > > Eric Scarfone, PhD, CNRS,
> > > Center for Hearing and communication Research
> > > Department of Clinical Neuroscience
> > > Karolinska Institutet
> > >
> > > Postal Address:
> > > CFH, M1:02
> > > Karolinska Hospital,
> > > SE-171 76 Stockholm, Sweden
> > >
> > > Work: +46 (0)8-517 79343,
> > > Cell: +46 (0)70 888 2352
> > > Fax: +46 (0)8-301876
> > >
> > > email: [hidden email]
> > > http://www.ki.se/cfh/
> > >
> > >
> > > ----- Original Message -----
> > > From: RICHARD BURRY <[hidden email]>
> > > Date: Friday, May 9, 2008 3:28 pm
> > > Subject: Re: interpolation Note of Caution
> > > To: [hidden email]
> > >
> > > Search the CONFOCAL archive at
> > > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
> > > > > face="Times New
> > > Roman">There are ethical limits as to what is
> > > allowed in
> > > manipulating micrographs. > > yes">
> > > Removing small unwanted objects is no different than
> > > adding
> > > small wanted objects.
> > > A
> > > great summary with examples is found in a Journal of Cell
> > > Biology
> > > article by Rossner and Yamada 2004 166:11-15 with the pdf
> > > available at
> > > http://www.jcb.org/cgi/reprint/166/1/11. > > spacerun:
> > > yes"> Journal editors are looking for these
> > > modifications
> > > because authors are misrepresentating their
> > > data!<?xml:namespace
> > > prefix = o ns = "urn:schemas-microsoft-
> > > com:office:office" /><o:p></o:p>
> > > Dick Burry Ohio State
> > > University -----
> > > Original Message ----- From: Zoltan Cseresnyes
> > > <[hidden email]> Date: Friday, May 9, 2008 8:33
> > > am Subject: Re: interpolation Note of Caution To:
> > > [hidden email] > > WEIGHT: normal;
> > > FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> > > #f5f8f0">>
> > > Search the CONFOCAL archive at
> > > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
> > > I'm
> > > completely with Jeremy on this subject, I don't think
> > > it's good
> > > practice to remove parts of your image just for its own
> > > sake. You can e.g. false-colour the real or the artificial
> > > pixels, in order to show the readers which objects to pay
> > > attention
> > > to. Just my 2c of course. > > style="FONT-WEIGHT:
> > > normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> > > #f5f8f0">> Zoltan 
> > > <DIV class=gmail_quote> > > FONT-SIZE:
> > > 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> > > On
> > > Fri, May 9, 2008 at 8:37 AM, Jeremy Adler <<A
> > >
> href="java_script:main.compose

('new','t=[hidden email]')"> >
target="1">[hidden email]> wrote:

> > > <BLOCKQUOTE class=gmail_quote style="PADDING-LEFT: 1ex;
> > > MARGIN: 0px
> > > 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"> > > WEIGHT:
> > > normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> > > #f5f8f0">> Search the CONFOCAL archive
> > > at <A
> > > href="http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal"
> > > target=1> > > FONT-
> > > STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> > > http://listserv.acsu.buffalo.edu/cgi-bin/wa?
> > > S1=confocal > > normal; FONT-SIZE:
> > > 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> > > Removal of artefacts. > > style="FONT-WEIGHT: normal;
> > > FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> > > #f5f8f0">>
> > > 1) Smooth your artefact free image, and use the mask
> > > to select
> > > the areas from the smoothed image that you wish to insert into
> > > the
> > > original. Only fiddle the problematic pixels. This will only
> > > work for
> > > small artefacts. 
> > > > > STYLE: normal;
> > > BACKGROUND-COLOR: #f5f8f0">> 
> > > However it
> > > is worth asking why you wish wish to 'improve' the appearance of
> > > your
> > > images and whether this is ethical. > > WEIGHT:
> > > normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> > > #f5f8f0">> At the very least a full
> > > description of why and how the published image differs from the
> > > original image must be given. > > normal;
> > > FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> > > #f5f8f0">>
> > > From your description you appear able to
> > > decide
> > > that some features are artefacts and define these features
> > > sufficiently well to accurately generate a mask. If we
> > > assume
> > > that the artefects simply obliterate any underlying signal then
> > > you
> > > have no knowledge of what might have been found in those pixels.
> > > And
> > > no legitimate basis for 'improving' your image. <FO
> > > NT style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE:
> > > normal;
> > > BACKGROUND-COLOR: #f5f8f0">> Zapping
> > > the
> > > artefacts and leaving clear and obvious blanks would be more
> > > legitimate than 'improving' the original, but I would strongly
> > > favour
> > > publishing the originals and explaining/highlighting the
> > > artefacts. > > 14px; FONT-
> > > STYLE: normal; BACKGROUND-COLOR: #f5f8f0">> Better
> > > yet deal
> > > with the source of the artefacts. > > style="FONT-WEIGHT:
> > > normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> > > #f5f8f0">> Jeremy Adler > > WEIGHT: normal;
> > > FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> > > #f5f8f0">>
> > > Cell Biology > > normal; FONT-SIZE:
> > > 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> > > The
> > > Wenner-Gren Inst. > > FONT-SIZE:
> > > 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> > > Arrhenius Laboratories E5 > > style="FONT-WEIGHT: normal;
> > > FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> > > #f5f8f0">>
> > > Stockholm University > > WEIGHT: normal; FONT-
> > > SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> > > Stockholm 106 91 > > normal; FONT-
> > > SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> > > Sweden > > normal; FONT-SIZE:
> > > 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> > > ________________________________ > > style="FONT-
> > > WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;
> BACKGROUND-
> > > COLOR:
> > > #f5f8f0">> From: Confocal Microscopy List on behalf
> > > of
> > > MODEL, MICHAEL > > SIZE: 14px;
> > > FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> > > Sent: Thu
> > > 5/8/2008 16:09 > > SIZE: 14px;
> > > FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">> </
> > > FONT>To: > > ('new','t=[hidden email]')"
> > > target="1">[hidden email] > > style="FONT-
> > > WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;
> BACKGROUND-
> > > COLOR:
> > > #f5f8f0">> Subject:
> > > inetrpolation > > style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;
> > > BACKGROUND-COLOR: #f5f8f0">> Search the CONFOCAL
> > > archive at
> > > http://listserv.acsu.buffalo.edu/cgi-
> > > bin/wa?S1=confocal"
> > > target=1>http://listserv.acsu.buffalo.edu/cgi-bin/wa?
> > > S1=confocal > > normal; FONT-SIZE:
> > > 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> > > Dear
> > > List - > > normal; FONT-SIZE:
> > > 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> > > Does
> > > anyone know of a software (preferably an ImageJ plug-in) that
> > > would
> > > fill areas generated by a mask to make them merge smoothly with
> > > the
> > > surrounding areas? > > T-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;
> > > BACKGROUND-
> > > COLOR: #f5f8f0">> For instance, a control image may
> > > be taken
> > > to identify artefacts. The question is, then, how to remove
> > > small
> > > unwanted objects from the main image without creating unsightly
> > > holes.
> > > Something like automatic "healing brush" in
> > > Photoshop. > > WEIGHT: normal; FONT-SIZE:
> > > 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> > > Michael Model, Ph.D. > > WEIGHT: normal;
> > > FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> > > #f5f8f0">>
> > > Confocal Microscopy Core > > style="FONT-WEIGHT:
> > > normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> > > #f5f8f0">> Dpt. Biological
> > > Sciences > > WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;
> BACKGROUND-
> > > COLOR:
> > > #f5f8f0">> Kent State
> > > University > > WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;
> BACKGROUND-COL
> > > OR: #f5f8f0">> Kent, OH 44242 > > style="FONT-
> > > WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;
> BACKGROUND-
> > > COLOR:
> > > #f5f8f0">> tel. 330-672-
> > > 2874 </BLOCKQUOTE> > > clear=all> > > style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;
> > > BACKGROUND-COLOR: #f5f8f0">> -- > > style="FONT-
> > > WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;
> BACKGROUND-
> > > COLOR:
> > > #f5f8f0">> -- > > normal; FONT-
> > > SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> > > Zoltan Cseresnyes > > normal; FONT-
> > > SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> > > Facility manager, Imaging Suite > > style="FONT-WEIGHT:
> > > normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> > > #f5f8f0">> Dept. of Zoology University of
> > >
> > >
> > > --
> > > BEGIN-ANTISPAM-VOTING-LINKS
> > > ------------------------------------------------------
> > >
> > > Teach CanIt if this mail (ID 598043969) is spam:
> > > Spam:
> > > https://antispam.osu.edu/b.php?c=s&i=598043969&m=454cda2ec162Not
> > > spam:
> https://antispam.osu.edu/b.php?c=n&i=598043969&m=454cda2ec162> >
> Forget vote:
> > > https://antispam.osu.edu/b.php?c=f&i=598043969&m=454cda2ec162--
> --
> > > --------------------------------------------------
> > > END-ANTISPAM-VOTING-LINKS
> > >
> >
> > Richard W. Burry, Ph.D.
> > Department of Neuroscience, College of Medicine
> > Campus Microscopy and Imaging Facility, Director
> > The Ohio State University
> > Associate Editor, Journal of Histochemistry and Cytochemistry
> > 3018 Graves Hall
> > 333 West Tenth Avenue
> > Columbus, Ohio 43210
> > Voice 614.292.2814 Cell 614.638.3345 Fax 614.688.8742
> >
>

Jerry Sedgewick-2

Re: old Biorad format

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Hi Eric,

I suspect that you are talking about Confocal Assistant, written for
opening PIC files, etc. That can be downloaded at our site:
http://bipl.umn.edu/downloads.

Jerry

Eric Scarfone wrote:

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> Hello all
> I vaguely recall a small program that would cut out the infamous
> original biorad format (MRC600, 2 channels side by side on the same
> image) into one two file stacks (one for each channel). Or was it a
> patch in Imaris or another software?
> If this exists can somebody point it out?
> Amicalement
> Erics
>
> Eric Scarfone, PhD, CNRS,
> Center for Hearing and communication Research
> Department of Clinical Neuroscience
> Karolinska Institutet
>
> Postal Address:
> CFH, M1:02
> Karolinska Hospital,
> SE-171 76 Stockholm, Sweden
>
> Work: +46 (0)8-517 79343,
> Cell: +46 (0)70 888 2352
> Fax: +46 (0)8-301876
>
> email: [hidden email]
> http://www.ki.se/cfh/
>
>
>

--- Get FREE High Speed Internet from USFamily.Net! -- http://www.usfamily.net/mkt-freepromo.html ---

Guy Cox

Re: old Biorad format

In reply to this post by Eric Scarfone

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

If you still have a system running the old Bio-Rad software it's very
simple
to write a macro to do this - I might even have one but I'd have to
search
through floppies to find it (we sold our two old Bio-Rads last year).
Let
me know if you'd like me to search - I certainly did write a macro for
this.

Guy

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On
Behalf Of Eric Scarfone
Sent: Wednesday, 14 May 2008 12:51 AM
To: [hidden email]
Subject: old Biorad format

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Hello all
I vaguely recall a small program that would cut out the infamous
original biorad format (MRC600, 2 channels side by side on the same
image) into one two file stacks (one for each channel). Or was it a
patch in Imaris or another software?
If this exists can somebody point it out?
Amicalement
Erics

Eric Scarfone, PhD, CNRS,
Center for Hearing and communication Research
Department of Clinical Neuroscience
Karolinska Institutet

Postal Address:
CFH, M1:02
Karolinska Hospital,
SE-171 76 Stockholm, Sweden

Work: +46 (0)8-517 79343,
Cell: +46 (0)70 888 2352
Fax: +46 (0)8-301876

email: [hidden email]
http://www.ki.se/cfh/

----- Original Message -----
From: Chris Tully <[hidden email]>
Date: Tuesday, May 13, 2008 0:57 am
Subject: Re: interpolation Note of Caution
To: [hidden email]

the

http://swehsc.pharmacy.arizona.edu/exppath/micro/digimage_ethics.html>

('new','t=[hidden email]')"> >
target="1">[hidden email]> wrote:

No virus found in this incoming message.
Checked by AVG.
Version: 7.5.524 / Virus Database: 269.23.16/1429 - Release Date:
12/05/2008 6:14 PM

Stephen Cody

Re: old Biorad format

In reply to this post by Eric Scarfone

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal RE: old Biorad format

Dear Eric,

I have a Bio-Rad macro to do this, it is part of the set of macros I wote and called "SOMBatch". But you'll need an old Bio-Rad to run it. It requires SOM or MPL running. This should be available on any MRC 500, 600 or 1000. A text document describing this macros and others and the macros is available to download at: http://www.ludwig.edu.au/confocal/Links.html

A description of the macro follows:

Zsplit.cmd

This command will separate a two channel image <ie. a side by side image>

into two files, and repeat the process for all the images in the z-series.

Cheers

Stephen H. Cody

Microscopy Manager

Central Resource for Advanced Microscopy

Ludwig Institute for Cancer Research

PO Box 2008 Royal Melbourne Hospital

Victoria, 3050

Australia

Tel: 61 3 9341 3155 Fax: 61 3 9341 3104

email: [hidden email]

www.ludwig.edu.au/labs/confocal.html

www.ludwig.edu.au/confocal

Tip: Learn how to receive reminders about you microscope booking:

www.ludwig.edu.au/confocal/Local/Booking_Hint.htm

-----Original Message-----
From: Confocal Microscopy List [[hidden email]] On Behalf Of Eric Scarfone
Sent: Wednesday, 14 May 2008 12:51 AM
To: [hidden email]
Subject: old Biorad format

Search the CONFOCAL archive at

http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Hello all

I vaguely recall a small program that would cut out the infamous

original biorad format (MRC600, 2 channels side by side on the same

image) into one two file stacks (one for each channel). Or was it a

patch in Imaris or another software?

If this exists can somebody point it out?

Amicalement

Erics

Eric Scarfone, PhD, CNRS,

Center for Hearing and communication Research

Department of Clinical Neuroscience

Karolinska Institutet

Postal Address:

CFH, M1:02

Karolinska Hospital,

SE-171 76 Stockholm, Sweden

Work: +46 (0)8-517 79343,

Cell: +46 (0)70 888 2352

Fax: +46 (0)8-301876

email: [hidden email]

http://www.ki.se/cfh/

----- Original Message -----

From: Chris Tully <[hidden email]>

Date: Tuesday, May 13, 2008 0:57 am

Subject: Re: interpolation Note of Caution

To: [hidden email]

> Search the CONFOCAL archive at

> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

> List members,

> First let me explain that although I am no longer associated with

> them, I

> have previously worked for Media Cybernetics.

> One extremely valuable set of features in Image-Pro Plus

> (www.mediacy.com)is the Audit Trail and Image or File Signature.

> The Audit Trail logs every

> action taken on every open image. This allows you to document

> exactly what

> was done with or to the image. The Image and File Signatures are

> 32 bit

> check sums that are automatically recorded in the Audit trail at

> relevanttimes (Acquisition, save, load...), and are sensitive

> enough to detect a

> change of +/- one gray level in one pixel! Paired with the

> Capture module's

> Auto Save function, it is possible to:

> 1) Document that a published image is unchanged. You will need to

> carefullytrack such things as cropping to demonstrate this

> completely, but this is

> entirely possible.

> 2) If the image has been altered use successive image signatures

> (before and

> after each alteration) to demonstrate that the logged alterations

> are the

> only ones that have occurred. If you are going to do this I would

> recommendsaving the image with a new name immediately before any

> such alteration so

> that you can demonstrate the alteration again if challenged.

> Another approach that I often use is to work on a duplicate of the

> originalimage. Change away as much as I need to to do the desired

> analysis. As the

> last step of my analysis though I generate outlines of the objects

> that I am

> measuring and place them back on the unaltered original image.

> This both

> allows me to make some measurements that can only be made on the

> originalimage and to demonstrate that the identified objects are

> still relevant to

> the original image and therefore to the sample.

> Chris

> --

> Chris Tully

> Microscopy and Image Analysis Expert

> [hidden email]

> 240-888-1021

> http://www.linkedin.com/in/christully

> On Mon, May 12, 2008 at 3:35 PM, RICHARD BURRY <[hidden email]>

> wrote:

> > Search the CONFOCAL archive at

> > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

> >

> > The guidelines Doug posted on the Univ. Arizona website are

> great. One

> > issue that makes digital images more suspect, is the individual

> element of

> > the image, the pixel, can be changed. With photographic

> manipulations we

> > were burning in regions not selectively changing the intensity

> of a single

> > pixel. Most journals today reserve the right to ask authors for

the

> > original image files that were taken on the CCD camera or came

> from the

> > confocal. As listed by Doug in his guidelines, it is most

> important to

> > retain archive files of ALL original images. This allows you to

> go back to

> > the original if needed.

> >

> > One mistake that authors are making in submitted manuscripts is to

> > saturate the intense pixels in images. The images look almost

> like line

> > drawings and not micrographs. It is important to keep all the

> information> in the images when processing and to adjust the

> settings when collecting

> > images to spread the intensity over the full range.

> >

> > Dick Burry

> > Ohio State University

> >

> > ----- Original Message -----

> > From: Doug Cromey <[hidden email]>

> > Date: Monday, May 12, 2008 12:54 pm

> > Subject: Re: interpolation Note of Caution

> > To: [hidden email]

> >

> > > Search the CONFOCAL archive at

> > > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

> > >

> > > I've been thinking about the issue of digital imaging ethics for

> > > awhile.Much of what we could get away with in the days of the

> > > photographic darkroom

> > > would no longer be considered appropriate these days. The

> > > JCB has pretty

> > > explicit digital image guidelines, I suspect that other journals

> > > that are

> > > without specific guidelines are probably "behind the

> > > curve".

> > >

> > > My take has always been that if you fully describe the steps

> > > that are taken

> > > in processing an image, then no one can accuse you of

> misconduct (1).

> > > Reviewers & Editors may not like your image processing protocol,

> > > but then it

> > > becomes an issue of scientific discussion, not an accusation.

> > >

> > > I've proposed some digital imaging ethical guidelines here:

> > >

http://swehsc.pharmacy.arizona.edu/exppath/micro/digimage_ethics.html>

> > > Some colleagues at the University of Alabama - Birmingham are

> > > working on a

> > > web site that includes these guidelines and a video case study,

> > > but it's not

> > > quite done yet. I'll post the URL when the folks at UAB

> > > let me know they

> > > are done.

> > >

> > > Doug Cromey

> > >

> > > (1) The HHS Office of Research Integrity officially defines

> scientific> > misconduct as: ".fabrication, falsification, or

> plagiarism> > in proposing,

> > > performing, or reviewing research, or in reporting research

> results."> >

> > > * Fabrication is making up data or results and recording or

> > > reporting them.

> > > * Falsification is manipulating research materials, equipment,

> > > or processes,

> > > or changing or omitting data or results such that the research

> > > is not

> > > accurately represented in the research record.

> > > * Plagiarism is the appropriation of another person's ideas,

> > > processes,results, or words without giving appropriate credit.

> > > * Research misconduct does not include differences of opinion.

> > >

> > > FROM: http://ori.hhs.gov/publications/ori_intro_text.shtml

> > >

> > > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

> > > Douglas W. Cromey, M.S. - Assistant Scientific Investigator

> > > Dept. of Cell Biology & Anatomy, University of Arizona

> > > 1501 N. Campbell Ave, Tucson, AZ 85724-5044 USA

> > >

> > > office: AHSC

> > > 4212 email:

> > > [hidden email]: 520-626-

> >

> > > 2824 fax: 520-626-2097

> > >

> > > http://swehsc.pharmacy.arizona.edu/exppath/

> > > Home of: "Microscopy and Imaging Resources on the WWW"

> > >

> > > -----Original Message-----

> > > From: Confocal Microscopy List

> > > [[hidden email]] On

> > > Behalf Of MODEL, MICHAEL

> > > Sent: Friday, May 09, 2008 7:43 AM

> > > To: [hidden email]

> > > Subject: Re: interpolation Note of Caution

> > >

> > > Search the CONFOCAL archive at

> > > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

> > >

> > > I certainly didn't' expect to start a big discussion of this

> > > topic. I

> > > agree that the Notes of Caution are fully justified. On the

> > > other hand,

> > > in Russ' Image Processing Handbook you will find many examples

> > > of very

> > > drastic editing of microscopic images, so in some situations it

> > > must be

> > > acceptable. Is it up to each journal to set up their own

> > > guidelines? It

> > > seems to me that so long as the author fully explained what

> had been

> > > done to the images it's not cheating, but I may be wrong. (I

> > > think we

> > > already had this discussion on this forum before).

> > >

> > > -----Original Message-----

> > > From: Confocal Microscopy List

> > > [[hidden email]] On

> > > Behalf Of Eric Scarfone

> > > Sent: Friday, May 09, 2008 9:46 AM

> > > To: [hidden email]

> > > Subject: Re: interpolation Note of Caution

> > >

> > > Search the CONFOCAL archive at

> > > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

> > >

> > > Hello all

> > > this problem certainly deserves a whole thread (it probably has

> > > been

> > > on this list before?).

> > > I wonder how one should consider techniques such as background

> > > subtraction that have been in use in video-microscopy even

> > > before the

> > > digital age!

> > > Isn't it also manipulation?

> > > Eric

> > >

> > > Eric Scarfone, PhD, CNRS,

> > > Center for Hearing and communication Research

> > > Department of Clinical Neuroscience

> > > Karolinska Institutet

> > >

> > > Postal Address:

> > > CFH, M1:02

> > > Karolinska Hospital,

> > > SE-171 76 Stockholm, Sweden

> > >

> > > Work: +46 (0)8-517 79343,

> > > Cell: +46 (0)70 888 2352

> > > Fax: +46 (0)8-301876

> > >

> > > email: [hidden email]

> > > http://www.ki.se/cfh/

> > >

> > > ----- Original Message -----

> > > From: RICHARD BURRY <[hidden email]>

> > > Date: Friday, May 9, 2008 3:28 pm

> > > Subject: Re: interpolation Note of Caution

> > > To: [hidden email]

> > >

> > > Search the CONFOCAL archive at

> > > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

> > > <FONT

> > > face="Times New

> > > Roman">There are ethical limits as to what is

> > > allowed in

> > > manipulating micrographs.<SPAN style="mso-spacerun:

> > > yes">

> > > Removing small unwanted objects is no different than

> > > adding

> > > small wanted objects.

> > > A

> > > great summary with examples is found in a Journal of Cell

> > > Biology

> > > article by Rossner and Yamada 2004 166:11-15 with the pdf

> > > available at

> > > http://www.jcb.org/cgi/reprint/166/1/11.<SPAN style="mso-

> > > spacerun:

> > > yes"> Journal editors are looking for these

> > > modifications

> > > because authors are misrepresentating their

> > > data!<?xml:namespace

> > > prefix = o ns = "urn:schemas-microsoft-

> > > com:office:office" /><o:p></o:p>

> > > Dick Burry Ohio State

> > > University -----

> > > Original Message ----- From: Zoltan Cseresnyes

> > > <[hidden email]> Date: Friday, May 9, 2008 8:33

> > > am Subject: Re: interpolation Note of Caution To:

> > > [hidden email] <FONT style="FONT-

> > > WEIGHT: normal;

> > > FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:

> > > #f5f8f0">>

> > > Search the CONFOCAL archive at

> > > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

> > > I'm

> > > completely with Jeremy on this subject, I don't think

> > > it's good

> > > practice to remove parts of your image just for its own

> > > sake. You can e.g. false-colour the real or the artificial

> > > pixels, in order to show the readers which objects to pay

> > > attention

> > > to. Just my 2c of course. <FONT

> > > style="FONT-WEIGHT:

> > > normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:

> > > #f5f8f0">> Zoltan

> > > <DIV class=gmail_quote><FONT style="FONT-WEIGHT: normal;

> > > FONT-SIZE:

> > > 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > On

> > > Fri, May 9, 2008 at 8:37 AM, Jeremy Adler <<A

> > >

> href="java_script:main.compose

('new','t=[hidden email]')"> >

target="1">[hidden email]> wrote:

> > > <BLOCKQUOTE class=gmail_quote style="PADDING-LEFT: 1ex;

> > > MARGIN: 0px

> > > 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><FONT style="FONT-

> > > WEIGHT:

> > > normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:

> > > #f5f8f0">> Search the CONFOCAL archive

> > > at <A

> > > href="http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal"

> > > target=1><FONT style="FONT-WEIGHT: normal; FONT-SIZE: 14px;

> > > FONT-

> > > STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > http://listserv.acsu.buffalo.edu/cgi-bin/wa?

> > > S1=confocal <FONT style="FONT-WEIGHT:

> > > normal; FONT-SIZE:

> > > 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > Removal of artefacts. <FONT

> > > style="FONT-WEIGHT: normal;

> > > FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:

> > > #f5f8f0">>

> > > 1) Smooth your artefact free image, and use the mask

> > > to select

> > > the areas from the smoothed image that you wish to insert into

> > > the

> > > original. Only fiddle the problematic pixels. This will only

> > > work for

> > > small artefacts.

> > > <FONT style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-

> > > STYLE: normal;

> > > BACKGROUND-COLOR: #f5f8f0">>

> > > However it

> > > is worth asking why you wish wish to 'improve' the appearance of

> > > your

> > > images and whether this is ethical. <FONT style="FONT-

> > > WEIGHT:

> > > normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:

> > > #f5f8f0">> At the very least a full

> > > description of why and how the published image differs from the

> > > original image must be given. <FONT style="FONT-WEIGHT:

> > > normal;

> > > FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:

> > > #f5f8f0">>

> > > From your description you appear able to

> > > decide

> > > that some features are artefacts and define these features

> > > sufficiently well to accurately generate a mask. If we

> > > assume

> > > that the artefects simply obliterate any underlying signal then

> > > you

> > > have no knowledge of what might have been found in those pixels.

> > > And

> > > no legitimate basis for 'improving' your image. <FO

> > > NT style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE:

> > > normal;

> > > BACKGROUND-COLOR: #f5f8f0">> Zapping

> > > the

> > > artefacts and leaving clear and obvious blanks would be more

> > > legitimate than 'improving' the original, but I would strongly

> > > favour

> > > publishing the originals and explaining/highlighting the

> > > artefacts. <FONT style="FONT-WEIGHT: normal; FONT-SIZE:

> > > 14px; FONT-

> > > STYLE: normal; BACKGROUND-COLOR: #f5f8f0">> Better

> > > yet deal

> > > with the source of the artefacts. <FONT

> > > style="FONT-WEIGHT:

> > > normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:

> > > #f5f8f0">> Jeremy Adler <FONT style="FONT-

> > > WEIGHT: normal;

> > > FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:

> > > #f5f8f0">>

> > > Cell Biology <FONT style="FONT-WEIGHT:

> > > normal; FONT-SIZE:

> > > 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > The

> > > Wenner-Gren Inst. <FONT style="FONT-WEIGHT: normal;

> > > FONT-SIZE:

> > > 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > Arrhenius Laboratories E5 <FONT

> > > style="FONT-WEIGHT: normal;

> > > FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:

> > > #f5f8f0">>

> > > Stockholm University <FONT style="FONT-

> > > WEIGHT: normal; FONT-

> > > SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > Stockholm 106 91 <FONT style="FONT-WEIGHT:

> > > normal; FONT-

> > > SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > Sweden <FONT style="FONT-WEIGHT:

> > > normal; FONT-SIZE:

> > > 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > ________________________________ <FONT

> > > style="FONT-

> > > WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;

> BACKGROUND-

> > > COLOR:

> > > #f5f8f0">> From: Confocal Microscopy List on behalf

> > > of

> > > MODEL, MICHAEL <FONT style="FONT-WEIGHT: normal; FONT-

> > > SIZE: 14px;

> > > FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > Sent: Thu

> > > 5/8/2008 16:09 <FONT style="FONT-WEIGHT: normal; FONT-

> > > SIZE: 14px;

> > > FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">> </

> > > FONT>To: > > ('new','t=[hidden email]')"

> > > target="1">[hidden email] <FONT

> > > style="FONT-

> > > WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;

> BACKGROUND-

> > > COLOR:

> > > #f5f8f0">> Subject:

> > > inetrpolation <FONT

> > > style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;

> > > BACKGROUND-COLOR: #f5f8f0">> Search the CONFOCAL

> > > archive at

> > > http://listserv.acsu.buffalo.edu/cgi-

> > > bin/wa?S1=confocal"

> > > target=1>http://listserv.acsu.buffalo.edu/cgi-bin/wa?

> > > S1=confocal <FONT style="FONT-WEIGHT:

> > > normal; FONT-SIZE:

> > > 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > Dear

> > > List - <FONT style="FONT-WEIGHT:

> > > normal; FONT-SIZE:

> > > 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > Does

> > > anyone know of a software (preferably an ImageJ plug-in) that

> > > would

> > > fill areas generated by a mask to make them merge smoothly with

> > > the

> > > surrounding areas? <FONT style="FON

> > > T-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;

> > > BACKGROUND-

> > > COLOR: #f5f8f0">> For instance, a control image may

> > > be taken

> > > to identify artefacts. The question is, then, how to remove

> > > small

> > > unwanted objects from the main image without creating unsightly

> > > holes.

> > > Something like automatic "healing brush" in

> > > Photoshop. <FONT style="FONT-

> > > WEIGHT: normal; FONT-SIZE:

> > > 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > Michael Model, Ph.D. <FONT style="FONT-

> > > WEIGHT: normal;

> > > FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:

> > > #f5f8f0">>

> > > Confocal Microscopy Core <FONT

> > > style="FONT-WEIGHT:

> > > normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:

> > > #f5f8f0">> Dpt. Biological

> > > Sciences <FONT style="FONT-

> > > WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;

> BACKGROUND-

> > > COLOR:

> > > #f5f8f0">> Kent State

> > > University <FONT style="FONT-

> > > WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;

> BACKGROUND-COL

> > > OR: #f5f8f0">> Kent, OH 44242 <FONT

> > > style="FONT-

> > > WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;

> BACKGROUND-

> > > COLOR:

> > > #f5f8f0">> tel. 330-672-

> > > 2874 </BLOCKQUOTE> <BR

> > > clear=all> <FONT

> > > style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;

> > > BACKGROUND-COLOR: #f5f8f0">> -- <FONT

> > > style="FONT-

> > > WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;

> BACKGROUND-

> > > COLOR:

> > > #f5f8f0">> -- <FONT style="FONT-WEIGHT:

> > > normal; FONT-

> > > SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > Zoltan Cseresnyes <FONT style="FONT-WEIGHT:

> > > normal; FONT-

> > > SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > Facility manager, Imaging Suite <FONT

> > > style="FONT-WEIGHT:

> > > normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:

> > > #f5f8f0">> Dept. of Zoology University of

> > >

> > > --

> > > BEGIN-ANTISPAM-VOTING-LINKS

> > > ------------------------------------------------------

> > >

> > > Teach CanIt if this mail (ID 598043969) is spam:

> > > Spam:

> > > https://antispam.osu.edu/b.php?c=s&i=598043969&m=454cda2ec162Not

> > > spam:

> https://antispam.osu.edu/b.php?c=n&i=598043969&m=454cda2ec162> >

> Forget vote:

> > > https://antispam.osu.edu/b.php?c=f&i=598043969&m=454cda2ec162--

> --

> > > --------------------------------------------------

> > > END-ANTISPAM-VOTING-LINKS

> > >

> >

> > Richard W. Burry, Ph.D.

> > Department of Neuroscience, College of Medicine

> > Campus Microscopy and Imaging Facility, Director

> > The Ohio State University

> > Associate Editor, Journal of Histochemistry and Cytochemistry

> > 3018 Graves Hall

> > 333 West Tenth Avenue

> > Columbus, Ohio 43210

> > Voice 614.292.2814 Cell 614.638.3345 Fax 614.688.8742

> >

This communication is intended only for the named recipient and may contain information that is confidential, legally privileged or subject to copyright; the Ludwig Institute for Cancer Research does not waiver any rights if you have received this communication in error.
The views expressed in this communication are those of the sender and do not necessarily reflect the views of the Ludwig Institute for Cancer Research.

Stephen Cody

Re: old Biorad format

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal RE: old Biorad format

Eric,

Here is a macro to Split side by Side images that will run in ImageJ. You’ll need the imageJ Bio-Rad Reader or the LOCI import tool.

------------------------------------------------cut here----------------------------------------------

// ZSplit Macro

//This command will separate a two channel image <ie. a side by side image>

//into two files, and repeat the process for all the images in a z-series.

//Stephen H. Cody 14-5-2008 [hidden email]

// Written by Stephen H. Cody

// Central Resource for Advanced Microscopy

// Ludwig Institute for Cancer Research

// Post Office Box 2008 Royal Melbourne Hospital

// Victoria 3050

// Australia

open("");

ImageDir = getDirectory("image");

ImageName = getTitle();

ImageWidth = getWidth();

ImageHeight = getHeight();

HalfWidth = ( ImageWidth / 2);

originallength = nSlices;

newImage("Left", "8-bit Black", HalfWidth, ImageHeight, originallength);

newImage("Right", "8-bit Black", HalfWidth, ImageHeight, originallength);

for(i=1;i<=originallength;i++){

selectWindow(ImageName);

setSlice(i);

makeRectangle(0, 0, HalfWidth, ImageHeight);

run("Copy");

selectWindow("Left");

setSlice(i);

run("Paste");

selectWindow(ImageName);

setSlice(i);

makeRectangle(HalfWidth, 0, HalfWidth, ImageHeight);

run("Copy");

selectWindow("Right");

setSlice(i);

run("Paste");

} //for loop

selectWindow("Left");

selectWindow("Right");

---------------------------------------------------------------------------cut here---------------------------------------------------------

Stephen H. Cody
Microscopy Manager
Central Resource for Advanced Microscopy
Ludwig Institute for Cancer Research
PO Box 2008 Royal Melbourne Hospital
Victoria, 3050
Australia
Tel: 61 3 9341 3155 Fax: 61 3 9341 3104
email: [hidden email]
www.ludwig.edu.au/labs/confocal.html
www.ludwig.edu.au/confocal

Tip: Learn how to receive reminders about you microscope booking:
www.ludwig.edu.au/confocal/Local/Booking_Hint.htm

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Stephen Cody
Sent: Wednesday, 14 May 2008 1:37 PM
To: [hidden email]
Subject: Re: old Biorad format

Dear Eric,

A description of the macro follows:

Zsplit.cmd

This command will separate a two channel image <ie. a side by side image>

into two files, and repeat the process for all the images in the z-series.

Cheers

Stephen H. Cody

Microscopy Manager

Central Resource for Advanced Microscopy

Ludwig Institute for Cancer Research

PO Box 2008 Royal Melbourne Hospital

Victoria, 3050

Australia

Tel: 61 3 9341 3155 Fax: 61 3 9341 3104

email: [hidden email]

www.ludwig.edu.au/labs/confocal.html

www.ludwig.edu.au/confocal

Tip: Learn how to receive reminders about you microscope booking:

www.ludwig.edu.au/confocal/Local/Booking_Hint.htm

-----Original Message-----
From: Confocal Microscopy List [[hidden email]] On Behalf Of Eric Scarfone
Sent: Wednesday, 14 May 2008 12:51 AM
To: [hidden email]
Subject: old Biorad format

Search the CONFOCAL archive at

http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Hello all

I vaguely recall a small program that would cut out the infamous

original biorad format (MRC600, 2 channels side by side on the same

image) into one two file stacks (one for each channel). Or was it a

patch in Imaris or another software?

If this exists can somebody point it out?

Amicalement

Erics

Eric Scarfone, PhD, CNRS,

Center for Hearing and communication Research

Department of Clinical Neuroscience

Karolinska Institutet

Postal Address:

CFH, M1:02

Karolinska Hospital,

SE-171 76 Stockholm, Sweden

Work: +46 (0)8-517 79343,

Cell: +46 (0)70 888 2352

Fax: +46 (0)8-301876

email: [hidden email]

http://www.ki.se/cfh/

----- Original Message -----

From: Chris Tully <[hidden email]>

Date: Tuesday, May 13, 2008 0:57 am

Subject: Re: interpolation Note of Caution

To: [hidden email]

> Search the CONFOCAL archive at

> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

> List members,

> First let me explain that although I am no longer associated with

> them, I

> have previously worked for Media Cybernetics.

> One extremely valuable set of features in Image-Pro Plus

> (www.mediacy.com)is the Audit Trail and Image or File Signature.

> The Audit Trail logs every

> action taken on every open image. This allows you to document

> exactly what

> was done with or to the image. The Image and File Signatures are

> 32 bit

> check sums that are automatically recorded in the Audit trail at

> relevanttimes (Acquisition, save, load...), and are sensitive

> enough to detect a

> change of +/- one gray level in one pixel! Paired with the

> Capture module's

> Auto Save function, it is possible to:

> 1) Document that a published image is unchanged. You will need to

> carefullytrack such things as cropping to demonstrate this

> completely, but this is

> entirely possible.

> 2) If the image has been altered use successive image signatures

> (before and

> after each alteration) to demonstrate that the logged alterations

> are the

> only ones that have occurred. If you are going to do this I would

> recommendsaving the image with a new name immediately before any

> such alteration so

> that you can demonstrate the alteration again if challenged.

> Another approach that I often use is to work on a duplicate of the

> originalimage. Change away as much as I need to to do the desired

> analysis. As the

> last step of my analysis though I generate outlines of the objects

> that I am

> measuring and place them back on the unaltered original image.

> This both

> allows me to make some measurements that can only be made on the

> originalimage and to demonstrate that the identified objects are

> still relevant to

> the original image and therefore to the sample.

> Chris

> --

> Chris Tully

> Microscopy and Image Analysis Expert

> [hidden email]

> 240-888-1021

> http://www.linkedin.com/in/christully

> On Mon, May 12, 2008 at 3:35 PM, RICHARD BURRY <[hidden email]>

> wrote:

> > Search the CONFOCAL archive at

> > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

> >

> > The guidelines Doug posted on the Univ. Arizona website are

> great. One

> > issue that makes digital images more suspect, is the individual

> element of

> > the image, the pixel, can be changed. With photographic

> manipulations we

> > were burning in regions not selectively changing the intensity

> of a single

> > pixel. Most journals today reserve the right to ask authors for

the

> > original image files that were taken on the CCD camera or came

> from the

> > confocal. As listed by Doug in his guidelines, it is most

> important to

> > retain archive files of ALL original images. This allows you to

> go back to

> > the original if needed.

> >

> > One mistake that authors are making in submitted manuscripts is to

> > saturate the intense pixels in images. The images look almost

> like line

> > drawings and not micrographs. It is important to keep all the

> information> in the images when processing and to adjust the

> settings when collecting

> > images to spread the intensity over the full range.

> >

> > Dick Burry

> > Ohio State University

> >

> > ----- Original Message -----

> > From: Doug Cromey <[hidden email]>

> > Date: Monday, May 12, 2008 12:54 pm

> > Subject: Re: interpolation Note of Caution

> > To: [hidden email]

> >

> > > Search the CONFOCAL archive at

> > > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

> > >

> > > I've been thinking about the issue of digital imaging ethics for

> > > awhile.Much of what we could get away with in the days of the

> > > photographic darkroom

> > > would no longer be considered appropriate these days. The

> > > JCB has pretty

> > > explicit digital image guidelines, I suspect that other journals

> > > that are

> > > without specific guidelines are probably "behind the

> > > curve".

> > >

> > > My take has always been that if you fully describe the steps

> > > that are taken

> > > in processing an image, then no one can accuse you of

> misconduct (1).

> > > Reviewers & Editors may not like your image processing protocol,

> > > but then it

> > > becomes an issue of scientific discussion, not an accusation.

> > >

> > > I've proposed some digital imaging ethical guidelines here:

> > >

http://swehsc.pharmacy.arizona.edu/exppath/micro/digimage_ethics.html>

> > > Some colleagues at the University of Alabama - Birmingham are

> > > working on a

> > > web site that includes these guidelines and a video case study,

> > > but it's not

> > > quite done yet. I'll post the URL when the folks at UAB

> > > let me know they

> > > are done.

> > >

> > > Doug Cromey

> > >

> > > (1) The HHS Office of Research Integrity officially defines

> scientific> > misconduct as: ".fabrication, falsification, or

> plagiarism> > in proposing,

> > > performing, or reviewing research, or in reporting research

> results."> >

> > > * Fabrication is making up data or results and recording or

> > > reporting them.

> > > * Falsification is manipulating research materials, equipment,

> > > or processes,

> > > or changing or omitting data or results such that the research

> > > is not

> > > accurately represented in the research record.

> > > * Plagiarism is the appropriation of another person's ideas,

> > > processes,results, or words without giving appropriate credit.

> > > * Research misconduct does not include differences of opinion.

> > >

> > > FROM: http://ori.hhs.gov/publications/ori_intro_text.shtml

> > >

> > > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

> > > Douglas W. Cromey, M.S. - Assistant Scientific Investigator

> > > Dept. of Cell Biology & Anatomy, University of Arizona

> > > 1501 N. Campbell Ave, Tucson, AZ 85724-5044 USA

> > >

> > > office: AHSC

> > > 4212 email:

> > > [hidden email]: 520-626-

> >

> > > 2824 fax: 520-626-2097

> > >

> > > http://swehsc.pharmacy.arizona.edu/exppath/

> > > Home of: "Microscopy and Imaging Resources on the WWW"

> > >

> > > -----Original Message-----

> > > From: Confocal Microscopy List

> > > [[hidden email]] On

> > > Behalf Of MODEL, MICHAEL

> > > Sent: Friday, May 09, 2008 7:43 AM

> > > To: [hidden email]

> > > Subject: Re: interpolation Note of Caution

> > >

> > > Search the CONFOCAL archive at

> > > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

> > >

> > > I certainly didn't' expect to start a big discussion of this

> > > topic. I

> > > agree that the Notes of Caution are fully justified. On the

> > > other hand,

> > > in Russ' Image Processing Handbook you will find many examples

> > > of very

> > > drastic editing of microscopic images, so in some situations it

> > > must be

> > > acceptable. Is it up to each journal to set up their own

> > > guidelines? It

> > > seems to me that so long as the author fully explained what

> had been

> > > done to the images it's not cheating, but I may be wrong. (I

> > > think we

> > > already had this discussion on this forum before).

> > >

> > > -----Original Message-----

> > > From: Confocal Microscopy List

> > > [[hidden email]] On

> > > Behalf Of Eric Scarfone

> > > Sent: Friday, May 09, 2008 9:46 AM

> > > To: [hidden email]

> > > Subject: Re: interpolation Note of Caution

> > >

> > > Search the CONFOCAL archive at

> > > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

> > >

> > > Hello all

> > > this problem certainly deserves a whole thread (it probably has

> > > been

> > > on this list before?).

> > > I wonder how one should consider techniques such as background

> > > subtraction that have been in use in video-microscopy even

> > > before the

> > > digital age!

> > > Isn't it also manipulation?

> > > Eric

> > >

> > > Eric Scarfone, PhD, CNRS,

> > > Center for Hearing and communication Research

> > > Department of Clinical Neuroscience

> > > Karolinska Institutet

> > >

> > > Postal Address:

> > > CFH, M1:02

> > > Karolinska Hospital,

> > > SE-171 76 Stockholm, Sweden

> > >

> > > Work: +46 (0)8-517 79343,

> > > Cell: +46 (0)70 888 2352

> > > Fax: +46 (0)8-301876

> > >

> > > email: [hidden email]

> > > http://www.ki.se/cfh/

> > >

> > > ----- Original Message -----

> > > From: RICHARD BURRY <[hidden email]>

> > > Date: Friday, May 9, 2008 3:28 pm

> > > Subject: Re: interpolation Note of Caution

> > > To: [hidden email]

> > >

> > > Search the CONFOCAL archive at

> > > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

> > > <FONT

> > > face="Times New

> > > Roman">There are ethical limits as to what is

> > > allowed in

> > > manipulating micrographs.<SPAN style="mso-spacerun:

> > > yes">

> > > Removing small unwanted objects is no different than

> > > adding

> > > small wanted objects.

> > > A

> > > great summary with examples is found in a Journal of Cell

> > > Biology

> > > article by Rossner and Yamada 2004 166:11-15 with the pdf

> > > available at

> > > http://www.jcb.org/cgi/reprint/166/1/11.<SPAN style="mso-

> > > spacerun:

> > > yes"> Journal editors are looking for these

> > > modifications

> > > because authors are misrepresentating their

> > > data!<?xml:namespace

> > > prefix = o ns = "urn:schemas-microsoft-

> > > com:office:office" /><o:p></o:p>

> > > Dick Burry Ohio State

> > > University -----

> > > Original Message ----- From: Zoltan Cseresnyes

> > > <[hidden email]> Date: Friday, May 9, 2008 8:33

> > > am Subject: Re: interpolation Note of Caution To:

> > > [hidden email] <FONT style="FONT-

> > > WEIGHT: normal;

> > > FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:

> > > #f5f8f0">>

> > > Search the CONFOCAL archive at

> > > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

> > > I'm

> > > completely with Jeremy on this subject, I don't think

> > > it's good

> > > practice to remove parts of your image just for its own

> > > sake. You can e.g. false-colour the real or the artificial

> > > pixels, in order to show the readers which objects to pay

> > > attention

> > > to. Just my 2c of course. <FONT

> > > style="FONT-WEIGHT:

> > > normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:

> > > #f5f8f0">> Zoltan

> > > <DIV class=gmail_quote><FONT style="FONT-WEIGHT: normal;

> > > FONT-SIZE:

> > > 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > On

> > > Fri, May 9, 2008 at 8:37 AM, Jeremy Adler <<A

> > >

> href="java_script:main.compose

('new','t=[hidden email]')"> >

target="1">[hidden email]> wrote:

> > > <BLOCKQUOTE class=gmail_quote style="PADDING-LEFT: 1ex;

> > > MARGIN: 0px

> > > 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><FONT style="FONT-

> > > WEIGHT:

> > > normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:

> > > #f5f8f0">> Search the CONFOCAL archive

> > > at <A

> > > href="http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal"

> > > target=1><FONT style="FONT-WEIGHT: normal; FONT-SIZE: 14px;

> > > FONT-

> > > STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > http://listserv.acsu.buffalo.edu/cgi-bin/wa?

> > > S1=confocal <FONT style="FONT-WEIGHT:

> > > normal; FONT-SIZE:

> > > 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > Removal of artefacts. <FONT

> > > style="FONT-WEIGHT: normal;

> > > FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:

> > > #f5f8f0">>

> > > 1) Smooth your artefact free image, and use the mask

> > > to select

> > > the areas from the smoothed image that you wish to insert into

> > > the

> > > original. Only fiddle the problematic pixels. This will only

> > > work for

> > > small artefacts.

> > > <FONT style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-

> > > STYLE: normal;

> > > BACKGROUND-COLOR: #f5f8f0">>

> > > However it

> > > is worth asking why you wish wish to 'improve' the appearance of

> > > your

> > > images and whether this is ethical. <FONT style="FONT-

> > > WEIGHT:

> > > normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:

> > > #f5f8f0">> At the very least a full

> > > description of why and how the published image differs from the

> > > original image must be given. <FONT style="FONT-WEIGHT:

> > > normal;

> > > FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:

> > > #f5f8f0">>

> > > From your description you appear able to

> > > decide

> > > that some features are artefacts and define these features

> > > sufficiently well to accurately generate a mask. If we

> > > assume

> > > that the artefects simply obliterate any underlying signal then

> > > you

> > > have no knowledge of what might have been found in those pixels.

> > > And

> > > no legitimate basis for 'improving' your image. <FO

> > > NT style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE:

> > > normal;

> > > BACKGROUND-COLOR: #f5f8f0">> Zapping

> > > the

> > > artefacts and leaving clear and obvious blanks would be more

> > > legitimate than 'improving' the original, but I would strongly

> > > favour

> > > publishing the originals and explaining/highlighting the

> > > artefacts. <FONT style="FONT-WEIGHT: normal; FONT-SIZE:

> > > 14px; FONT-

> > > STYLE: normal; BACKGROUND-COLOR: #f5f8f0">> Better

> > > yet deal

> > > with the source of the artefacts. <FONT

> > > style="FONT-WEIGHT:

> > > normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:

> > > #f5f8f0">> Jeremy Adler <FONT style="FONT-

> > > WEIGHT: normal;

> > > FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:

> > > #f5f8f0">>

> > > Cell Biology <FONT style="FONT-WEIGHT:

> > > normal; FONT-SIZE:

> > > 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > The

> > > Wenner-Gren Inst. <FONT style="FONT-WEIGHT: normal;

> > > FONT-SIZE:

> > > 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > Arrhenius Laboratories E5 <FONT

> > > style="FONT-WEIGHT: normal;

> > > FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:

> > > #f5f8f0">>

> > > Stockholm University <FONT style="FONT-

> > > WEIGHT: normal; FONT-

> > > SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > Stockholm 106 91 <FONT style="FONT-WEIGHT:

> > > normal; FONT-

> > > SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > Sweden <FONT style="FONT-WEIGHT:

> > > normal; FONT-SIZE:

> > > 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > ________________________________ <FONT

> > > style="FONT-

> > > WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;

> BACKGROUND-

> > > COLOR:

> > > #f5f8f0">> From: Confocal Microscopy List on behalf

> > > of

> > > MODEL, MICHAEL <FONT style="FONT-WEIGHT: normal; FONT-

> > > SIZE: 14px;

> > > FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > Sent: Thu

> > > 5/8/2008 16:09 <FONT style="FONT-WEIGHT: normal; FONT-

> > > SIZE: 14px;

> > > FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">> </

> > > FONT>To: > > ('new','t=[hidden email]')"

> > > target="1">[hidden email] <FONT

> > > style="FONT-

> > > WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;

> BACKGROUND-

> > > COLOR:

> > > #f5f8f0">> Subject:

> > > inetrpolation <FONT

> > > style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;

> > > BACKGROUND-COLOR: #f5f8f0">> Search the CONFOCAL

> > > archive at

> > > http://listserv.acsu.buffalo.edu/cgi-

> > > bin/wa?S1=confocal"

> > > target=1>http://listserv.acsu.buffalo.edu/cgi-bin/wa?

> > > S1=confocal <FONT style="FONT-WEIGHT:

> > > normal; FONT-SIZE:

> > > 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > Dear

> > > List - <FONT style="FONT-WEIGHT:

> > > normal; FONT-SIZE:

> > > 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > Does

> > > anyone know of a software (preferably an ImageJ plug-in) that

> > > would

> > > fill areas generated by a mask to make them merge smoothly with

> > > the

> > > surrounding areas? <FONT style="FON

> > > T-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;

> > > BACKGROUND-

> > > COLOR: #f5f8f0">> For instance, a control image may

> > > be taken

> > > to identify artefacts. The question is, then, how to remove

> > > small

> > > unwanted objects from the main image without creating unsightly

> > > holes.

> > > Something like automatic "healing brush" in

> > > Photoshop. <FONT style="FONT-

> > > WEIGHT: normal; FONT-SIZE:

> > > 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > Michael Model, Ph.D. <FONT style="FONT-

> > > WEIGHT: normal;

> > > FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:

> > > #f5f8f0">>

> > > Confocal Microscopy Core <FONT

> > > style="FONT-WEIGHT:

> > > normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:

> > > #f5f8f0">> Dpt. Biological

> > > Sciences <FONT style="FONT-

> > > WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;

> BACKGROUND-

> > > COLOR:

> > > #f5f8f0">> Kent State

> > > University <FONT style="FONT-

> > > WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;

> BACKGROUND-COL

> > > OR: #f5f8f0">> Kent, OH 44242 <FONT

> > > style="FONT-

> > > WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;

> BACKGROUND-

> > > COLOR:

> > > #f5f8f0">> tel. 330-672-

> > > 2874 </BLOCKQUOTE> <BR

> > > clear=all> <FONT

> > > style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;

> > > BACKGROUND-COLOR: #f5f8f0">> -- <FONT

> > > style="FONT-

> > > WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;

> BACKGROUND-

> > > COLOR:

> > > #f5f8f0">> -- <FONT style="FONT-WEIGHT:

> > > normal; FONT-

> > > SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > Zoltan Cseresnyes <FONT style="FONT-WEIGHT:

> > > normal; FONT-

> > > SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>

> > > Facility manager, Imaging Suite <FONT

> > > style="FONT-WEIGHT:

> > > normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:

> > > #f5f8f0">> Dept. of Zoology University of

> > >

> > > --

> > > BEGIN-ANTISPAM-VOTING-LINKS

> > > ------------------------------------------------------

> > >

> > > Teach CanIt if this mail (ID 598043969) is spam:

> > > Spam:

> > > https://antispam.osu.edu/b.php?c=s&i=598043969&m=454cda2ec162Not

> > > spam:

> https://antispam.osu.edu/b.php?c=n&i=598043969&m=454cda2ec162> >

> Forget vote:

> > > https://antispam.osu.edu/b.php?c=f&i=598043969&m=454cda2ec162--

> --

> > > --------------------------------------------------

> > > END-ANTISPAM-VOTING-LINKS

> > >

> >

> > Richard W. Burry, Ph.D.

> > Department of Neuroscience, College of Medicine

> > Campus Microscopy and Imaging Facility, Director

> > The Ohio State University

> > Associate Editor, Journal of Histochemistry and Cytochemistry

> > 3018 Graves Hall

> > 333 West Tenth Avenue

> > Columbus, Ohio 43210

> > Voice 614.292.2814 Cell 614.638.3345 Fax 614.688.8742

> >

Guy Cox

Re: old Biorad format

In reply to this post by Jerry Sedgewick-2

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

I just checked, and it seems that Confocal Assistant does indeed also
split those side-by-side files. So now Eric has at least 3 options!

Guy

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On
Behalf Of Jerry Sedgewick
Sent: Wednesday, 14 May 2008 1:59 AM
To: [hidden email]
Subject: Re: old Biorad format

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Hi Eric,

I suspect that you are talking about Confocal Assistant, written for
opening PIC files, etc. That can be downloaded at our site:
http://bipl.umn.edu/downloads.

Jerry

Eric Scarfone wrote:

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No virus found in this incoming message.
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12/05/2008 6:14 PM

Eric Scarfone

Re: old Biorad format

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Thanks Guy, Stephen et al.!
I had also a macro but lost it when I moved and the old system was
dismantled.... long time ago.
I will check good old CAS!

I believe though that an older version of Imaris had the option "split
Biorad MRC600 images" but I am not so sure. Maybe it was lasersharp??
Greetings

Eric Scarfone, PhD, CNRS,
Center for Hearing and communication Research
Department of Clinical Neuroscience
Karolinska Institutet

Postal Address:
CFH, M1:02
Karolinska Hospital,
SE-171 76 Stockholm, Sweden

Work: +46 (0)8-517 79343,
Cell: +46 (0)70 888 2352
Fax: +46 (0)8-301876

email: [hidden email]
http://www.ki.se/cfh/

----- Original Message -----
From: Guy Cox <[hidden email]>
Date: Wednesday, May 14, 2008 7:42 am
Subject: Re: old Biorad format
To: [hidden email]

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> I just checked, and it seems that Confocal Assistant does indeed also
> split those side-by-side files. So now Eric has at least 3 options!
>
> Guy
>
>
> -----Original Message-----
> From: Confocal Microscopy List
> [mailto:[hidden email]] On
> Behalf Of Jerry Sedgewick
> Sent: Wednesday, 14 May 2008 1:59 AM
> To: [hidden email]
> Subject: Re: old Biorad format
>
> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> Hi Eric,
>
> I suspect that you are talking about Confocal Assistant, written
> for
> opening PIC files, etc. That can be downloaded at our site:
> http://bipl.umn.edu/downloads.
>
> Jerry
>
>
> Eric Scarfone wrote:
> > Search the CONFOCAL archive at
> > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
> >
> > Hello all
> > I vaguely recall a small program that would cut out the infamous
> > original biorad format (MRC600, 2 channels side by side on the
> same
> > image) into one two file stacks (one for each channel). Or was
> it a
> > patch in Imaris or another software?
> > If this exists can somebody point it out?
> > Amicalement
> > Erics
> >
> > Eric Scarfone, PhD, CNRS,
> > Center for Hearing and communication Research
> > Department of Clinical Neuroscience
> > Karolinska Institutet
> >
> > Postal Address:
> > CFH, M1:02
> > Karolinska Hospital,
> > SE-171 76 Stockholm, Sweden
> >
> > Work: +46 (0)8-517 79343,
> > Cell: +46 (0)70 888 2352
> > Fax: +46 (0)8-301876
> >
> > email: [hidden email]
> > http://www.ki.se/cfh/
> >
> >
> >
>
>
>
>
> --- Get FREE High Speed Internet from USFamily.Net! --
> http://www.usfamily.net/mkt-freepromo.html ---
>
> No virus found in this incoming message.
> Checked by AVG.
> Version: 7.5.524 / Virus Database: 269.23.16/1429 - Release Date:
> 12/05/2008 6:14 PM
>
>