supplimental digital image software on a confocal

[Cromey, Douglas W - (dcromey)]

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I have a user here who has requested that I install GIMP on our LSM510 confocal.  He has some low-mag images of brain (acquired elsewhere) that he wants to annotate as he jumps up in mag to capture his confocal images from specific areas.  I have had Infranview on the system as a file viewer, but it doesn't allow him to add boxes or move them around with text.  Nothing against GIMP, but it's overkill for what he needs to do.  Is there a Windows XP compatible freeware that you could recommend?

Doug

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Douglas W. Cromey, M.S. - Associate Scientific Investigator
Dept. of Cellular & Molecular Medicine, University of Arizona
1501 N. Campbell Ave, Tucson, AZ  85724-5044 USA

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

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

[Pedro Almada]

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Hi,

Try Paint.net <http://www.getpaint.net/>. It's quite light.

Best,
Pedro


On 7 January 2013 22:18, Cromey, Douglas W - (dcromey) <
[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> I have a user here who has requested that I install GIMP on our LSM510
> confocal.  He has some low-mag images of brain (acquired elsewhere) that he
> wants to annotate as he jumps up in mag to capture his confocal images from
> specific areas.  I have had Infranview on the system as a file viewer, but
> it doesn't allow him to add boxes or move them around with text.  Nothing
> against GIMP, but it's overkill for what he needs to do.  Is there a
> Windows XP compatible freeware that you could recommend?
>
> Doug
>
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> Douglas W. Cromey, M.S. - Associate Scientific Investigator
> Dept. of Cellular & Molecular Medicine, University of Arizona
> 1501 N. Campbell Ave, Tucson, AZ  85724-5044 USA
>
> office:  AHSC 4212         email: [hidden email]
> voice:  520-626-2824       fax:  [phone]
>
> http://swehsc.pharmacy.arizona.edu/micro
> Home of: "Microscopy and Imaging Resources on the WWW"
>

[Cameron Nowell-2]

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Why not just use the paint program built into windows? It will open tif images as long as they are RGB colour.


Cameron J. Nowell
Centre for Dynamic Imaging
The Walter and Eliza Hall Institute of Medical Research 1G Royal Parade Parkville, Victoria 3052 Australia

Phone: [phone]
Mobile: [phone]
Fax: [phone]

Facility Website
LinkedIn Profile

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Cromey, Douglas W - (dcromey)
Sent: Tuesday, 8 January 2013 9:19 AM
To: [hidden email]
Subject: supplimental digital image software on a confocal

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I have a user here who has requested that I install GIMP on our LSM510 confocal.  He has some low-mag images of brain (acquired elsewhere) that he wants to annotate as he jumps up in mag to capture his confocal images from specific areas.  I have had Infranview on the system as a file viewer, but it doesn't allow him to add boxes or move them around with text.  Nothing against GIMP, but it's overkill for what he needs to do.  Is there a Windows XP compatible freeware that you could recommend?

Doug

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Douglas W. Cromey, M.S. - Associate Scientific Investigator Dept. of Cellular & Molecular Medicine, University of Arizona
1501 N. Campbell Ave, Tucson, AZ  85724-5044 USA

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

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

______________________________________________________________________
The information in this email is confidential and intended solely for the addressee.
You must not disclose, forward, print or use it without the permission of the sender.
______________________________________________________________________

[Diego De Stefani]

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I think that ImageJ can do the job. As an alternative, try Paint.net
http://www.getpaint.net
IMHO, it's powerful, fast and freeware

On Tue, Jan 8, 2013 at 12:44 AM, Cameron Nowell
<[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Why not just use the paint program built into windows? It will open tif images as long as they are RGB colour.
>
>
> Cameron J. Nowell
> Centre for Dynamic Imaging
> The Walter and Eliza Hall Institute of Medical Research 1G Royal Parade Parkville, Victoria 3052 Australia
>
> Phone: [phone]
> Mobile: [phone]
> Fax: [phone]
>
> Facility Website
> LinkedIn Profile
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Cromey, Douglas W - (dcromey)
> Sent: Tuesday, 8 January 2013 9:19 AM
> To: [hidden email]
> Subject: supplimental digital image software on a confocal
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> I have a user here who has requested that I install GIMP on our LSM510 confocal.  He has some low-mag images of brain (acquired elsewhere) that he wants to annotate as he jumps up in mag to capture his confocal images from specific areas.  I have had Infranview on the system as a file viewer, but it doesn't allow him to add boxes or move them around with text.  Nothing against GIMP, but it's overkill for what he needs to do.  Is there a Windows XP compatible freeware that you could recommend?
>
> Doug
>
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> Douglas W. Cromey, M.S. - Associate Scientific Investigator Dept. of Cellular & Molecular Medicine, University of Arizona
> 1501 N. Campbell Ave, Tucson, AZ  85724-5044 USA
>
> office:  AHSC 4212         email: [hidden email]
> voice:  520-626-2824       fax:  [phone]
>
> http://swehsc.pharmacy.arizona.edu/micro
> Home of: "Microscopy and Imaging Resources on the WWW"
>
> ______________________________________________________________________
> The information in this email is confidential and intended solely for the addressee.
> You must not disclose, forward, print or use it without the permission of the sender.
> ______________________________________________________________________

--
Diego De Stefani, PhD
Dept. of Biomedical Sciences
University of Padova
Via G. Colombo 3, 35131 Padova - ITALY

[Keith Morris]

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Hi Douglas,

GIMP is free and similar to Photoshop so I can't see a problem running that
with the confocal LMS 510 software if that's what they wish to do. We have
both GIMP and Adobe Photoshop Elements 11 installed on our 510 MetaHead
confocal system.

However for just adding text and arrows and moveable scalable boxes why not
use the LMS 510 software itself to annotate the images, after all it has
text, arrows,  boxes,  freedraw ROIs, change colours options etc.. It's all
there in the image window via the Overlay button. You can import any
standard photo image via LMS 510's File, Import option as well as directly
capture confocal images and annotate them as well. So you can have your
whole brain annoted images within the same software as the image capture. I
find LMS 510 easier (quicker) than GIMP or Photoshop for this sort of thing
(plus you can add a scale bar, and all this available for free offline on
the Office PC as well via Zeiss LMS Browser - Windows PCs only).

Hope this helps.

Regards

Keith

-----------------------------------------------------------
Dr Keith J Morris
The Microscopy Core,
The Wellcome Trust Centre for Human Genetics,
Roosevelt Drive,
Oxford,
OX3 7BN,
United Kingdom.

Tel:  +44   ( 0 ) 1865  287568
Email:   [hidden email]
http://www.well.ox.ac.uk/microscopy-core-2

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On
Behalf Of Cromey, Douglas W - (dcromey)
Sent: 07 January 2013 22:19
To: [hidden email]
Subject: supplimental digital image software on a confocal

*****
To join, leave or search the confocal microscopy listserv, go to:
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*****

I have a user here who has requested that I install GIMP on our LSM510
confocal.  He has some low-mag images of brain (acquired elsewhere) that he
wants to annotate as he jumps up in mag to capture his confocal images from
specific areas.  I have had Infranview on the system as a file viewer, but
it doesn't allow him to add boxes or move them around with text.  Nothing
against GIMP, but it's overkill for what he needs to do.  Is there a Windows
XP compatible freeware that you could recommend?

Doug

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Douglas W. Cromey, M.S. - Associate Scientific Investigator Dept. of
Cellular & Molecular Medicine, University of Arizona
1501 N. Campbell Ave, Tucson, AZ  85724-5044 USA

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

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

[Guy Cox-2]

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Well, I wouldn't run a high-end graphics programme on a confocal microscope - too many memory conflict issues.  I'll probably be pilloried for saying especially on a Zeiss 510, but it is a system which is deeply embedded in the OS.

What I would recommend is that the user takes his notebook or iPad into the microscope room and does his (her) annotations on that.

                               Guy

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Keith Morris
Sent: Tuesday, 8 January 2013 10:01 PM
To: [hidden email]
Subject: Re: supplimental digital image software on a confocal

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Hi Douglas,

GIMP is free and similar to Photoshop so I can't see a problem running that
with the confocal LMS 510 software if that's what they wish to do. We have
both GIMP and Adobe Photoshop Elements 11 installed on our 510 MetaHead
confocal system.

However for just adding text and arrows and moveable scalable boxes why not
use the LMS 510 software itself to annotate the images, after all it has
text, arrows,  boxes,  freedraw ROIs, change colours options etc.. It's all
there in the image window via the Overlay button. You can import any
standard photo image via LMS 510's File, Import option as well as directly
capture confocal images and annotate them as well. So you can have your
whole brain annoted images within the same software as the image capture. I
find LMS 510 easier (quicker) than GIMP or Photoshop for this sort of thing
(plus you can add a scale bar, and all this available for free offline on
the Office PC as well via Zeiss LMS Browser - Windows PCs only).

Hope this helps.

Regards

Keith

-----------------------------------------------------------
Dr Keith J Morris
The Microscopy Core,
The Wellcome Trust Centre for Human Genetics,
Roosevelt Drive,
Oxford,
OX3 7BN,
United Kingdom.

Tel:  +44   ( 0 ) 1865  287568
Email:   [hidden email]
http://www.well.ox.ac.uk/microscopy-core-2

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On
Behalf Of Cromey, Douglas W - (dcromey)
Sent: 07 January 2013 22:19
To: [hidden email]
Subject: supplimental digital image software on a confocal

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

I have a user here who has requested that I install GIMP on our LSM510
confocal.  He has some low-mag images of brain (acquired elsewhere) that he
wants to annotate as he jumps up in mag to capture his confocal images from
specific areas.  I have had Infranview on the system as a file viewer, but
it doesn't allow him to add boxes or move them around with text.  Nothing
against GIMP, but it's overkill for what he needs to do.  Is there a Windows
XP compatible freeware that you could recommend?

Doug

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Douglas W. Cromey, M.S. - Associate Scientific Investigator Dept. of
Cellular & Molecular Medicine, University of Arizona
1501 N. Campbell Ave, Tucson, AZ  85724-5044 USA

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

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

[mcammer]

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Zeiss Zen software has annotation tools built in as noted below.  

I also keep ImageJ on all microscope platforms.  Haven't had any conflicts.

_________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: [phone]  Cell: [phone]

[Tim Feinstein-2]

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ImageJ can 'burn' shapes, but text is awkward and I do not know an easy way to change or remove annotations after the fact like you can using 'layers' in Photoshop or GIMP.  Like most proprietary microscope software, the Nikon Elements that we use has an annotation package that works well for basic stuff and it all goes on a removable 'layer'.  Like others I'd recommend starting with whatever comes with the scope.  

all the best,


TF

Timothy Feinstein, PhD
Visiting Research Associate
Laboratory for GPCR Biology
Dept. of Pharmacology & Chemical Biology
University of Pittsburgh, School of Medicine
BST W1301, 200 Lothrop St.
Pittsburgh, PA  15261

On Jan 8, 2013, at 9:29 AM, Cammer, Michael wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Zeiss Zen software has annotation tools built in as noted below.  
>
> I also keep ImageJ on all microscope platforms.  Haven't had any conflicts.
>
> _________________________________________
> Michael Cammer, Assistant Research Scientist
> Skirball Institute of Biomolecular Medicine
> Lab: [phone]  Cell: [phone]

[John Oreopoulos]

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Tim,

The latest versions of ImageJ have a non-destructive overlay feature that allows one to add text and drawn objects onto an image and turn these on and off on the image at will. See documentation here:

http://rsbweb.nih.gov/ij/docs/guide/146-11.html#toc-Section-11

Cheers,

John Oreopoulos
Staff Scientist
Spectral Applied Research
Richmond Hill, Ontario
Canada
www.spectral.ca


On 2013-01-08, at 10:09 AM, Tim Feinstein wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> ImageJ can 'burn' shapes, but text is awkward and I do not know an easy way to change or remove annotations after the fact like you can using 'layers' in Photoshop or GIMP.  Like most proprietary microscope software, the Nikon Elements that we use has an annotation package that works well for basic stuff and it all goes on a removable 'layer'.  Like others I'd recommend starting with whatever comes with the scope.  
>
> all the best,
>
>
> TF
>
> Timothy Feinstein, PhD
> Visiting Research Associate
> Laboratory for GPCR Biology
> Dept. of Pharmacology & Chemical Biology
> University of Pittsburgh, School of Medicine
> BST W1301, 200 Lothrop St.
> Pittsburgh, PA  15261
>
> On Jan 8, 2013, at 9:29 AM, Cammer, Michael wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> Zeiss Zen software has annotation tools built in as noted below.  
>>
>> I also keep ImageJ on all microscope platforms.  Haven't had any conflicts.
>>
>> _________________________________________
>> Michael Cammer, Assistant Research Scientist
>> Skirball Institute of Biomolecular Medicine
>> Lab: [phone]  Cell: [phone]

[Christian-103]

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I believe FigureJ is an ImageJ plugin specifically for use with the output files on the Zeiss system.

http://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:figurej:start


Christian


--- On Tue, 1/8/13, Cammer, Michael <[hidden email]> wrote:

From: Cammer, Michael <[hidden email]>
Subject: Re: supplimental digital image software on a confocal
To: [hidden email]
Date: Tuesday, January 8, 2013, 8:29 AM

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Zeiss Zen software has annotation tools built in as noted below. 

I also keep ImageJ on all microscope platforms.  Haven't had any conflicts.

_________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: [phone]  Cell: [phone]

[Jerry (Gerald) Sedgewick]

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I'd stick with Zen or ImageJ to avoid issues that might arise when
12-bit images saved in a 16-bit format are opened in programs that only
read 8-bit, like GIMP (I suspect that the Zeiss images retain 12-bits of
tonal information). There's always the possibility (danger) that the
image used for notation becomes the final image in publication, and a
reduction in tonal resolution will be carried forward.

Jerry



On 1/8/2013 9:33 AM, Christian wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> I believe FigureJ is an ImageJ plugin specifically for use with the output files on the Zeiss system.
>
> http://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:figurej:start
>
>
> Christian
>
>
> --- On Tue, 1/8/13, Cammer, Michael <[hidden email]> wrote:
>
> From: Cammer, Michael <[hidden email]>
> Subject: Re: supplimental digital image software on a confocal
> To: [hidden email]
> Date: Tuesday, January 8, 2013, 8:29 AM
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Zeiss Zen software has annotation tools built in as noted below.
>
> I also keep ImageJ on all microscope platforms.  Haven't had any conflicts.
>
> _________________________________________
> Michael Cammer, Assistant Research Scientist
> Skirball Institute of Biomolecular Medicine
> Lab: [phone]  Cell: [phone]
>

--
Jerry (Gerald) Sedgewick
Scientific Imaging & Image Analysis Consultant
Technical Writer / Regulatory Consultant
965 Cromwell Avenue
Saint Paul, MN  55114
651-788-2261
http://www.imagingandanalysis.com
http://www.quickphotoshop.com
Author: “Scientific Imaging with Photoshop: Methods, Measurement and Output”

[Steffen Dietzel]

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Doug,

you don't write why you don't want to have Gimp on the system and I
could imagine several.

If it is beacuse of the installation:
There is a portable version of Gimp that does not need to be installed.
http://portableapps.com/apps/graphics_pictures/gimp_portable

Actually, the user could put that on a USB stick and use it without you
even knowing it...

Disclaimer: I have used several such portable apps myself, but not this one.

Steffen


On 07.01.2013 23:18, Cromey, Douglas W - (dcromey) wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> I have a user here who has requested that I install GIMP on our LSM510 confocal.  He has some low-mag images of brain (acquired elsewhere) that he wants to annotate as he jumps up in mag to capture his confocal images from specific areas.  I have had Infranview on the system as a file viewer, but it doesn't allow him to add boxes or move them around with text.  Nothing against GIMP, but it's overkill for what he needs to do.  Is there a Windows XP compatible freeware that you could recommend?
>
> Doug
>
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> Douglas W. Cromey, M.S. - Associate Scientific Investigator
> Dept. of Cellular&  Molecular Medicine, University of Arizona
> 1501 N. Campbell Ave, Tucson, AZ  85724-5044 USA
>
> office:  AHSC 4212         email: [hidden email]
> voice:  520-626-2824       fax:  [phone]
>
> http://swehsc.pharmacy.arizona.edu/micro
> Home of: "Microscopy and Imaging Resources on the WWW"
>

--
------------------------------------------------------------
Steffen Dietzel, PD Dr. rer. nat
Ludwig-Maximilians-Universität München
Walter-Brendel-Zentrum für experimentelle Medizin (WBex)
Head of light microscopy

Mail room:
Marchioninistr. 15, D-81377 München

Building location:
Marchioninistr. 27,  München-Großhadern

[Jerome Mutterer]

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Dear all,

FigureJ specializes in building article figures in a snap. The file format
reading ability in FigureJ is provided by ImageJ base readers or by the
excellent LOCI Bioformats library (http://loci.wisc.edu/software/bio-formats),
so it can handle all kinds of images.

The Zeiss logo on the FigureJ web page ( http://www.figurej.org )
acknowledges Carl Zeiss Microscopy support to the FigureJ project as part
of their Open Application Development initiative.
http://microscopy.zeiss.com/microscopy/en_de/news/press-release-oad.html

Jerome.



On 8 January 2013 16:33, Christian <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> I believe FigureJ is an ImageJ plugin specifically for use with the output
> files on the Zeiss system.
>
> http://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:figurej:start
>
>
> Christian
>
>
> --- On Tue, 1/8/13, Cammer, Michael <[hidden email]> wrote:
>
> From: Cammer, Michael <[hidden email]>
> Subject: Re: supplimental digital image software on a confocal
> To: [hidden email]
> Date: Tuesday, January 8, 2013, 8:29 AM
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Zeiss Zen software has annotation tools built in as noted below.
>
> I also keep ImageJ on all microscope platforms.  Haven't had any conflicts.
>
> _________________________________________
> Michael Cammer, Assistant Research Scientist
> Skirball Institute of Biomolecular Medicine
> Lab: [phone]  Cell: [phone]
>