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ethics and imaging

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Gisele Giorgi

ethics and imaging

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

Doug

thank you for the excellent article and links: i'll use it in a
course i teach.
Gisele Giorgi
Merritt College

>There are 3 messages totalling 1304 lines in this issue.
>
>Topics of the day:
>
> 1. interpolation Note of Caution (3)
>
>----------------------------------------------------------------------
>
>Date: Mon, 12 May 2008 09:43:06 -0700
>From: Doug Cromey <[hidden email]>
>Subject: 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
>Roman">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.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-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.   normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
>#f5f8f0">> Zoltan 
><DIV class=gmail_quote>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">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>STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
>http://listserv.acsu.buffalo.edu/cgi-bin/wa?
>S1=confocal</A> 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
>Removal of artefacts. 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. 
>BACKGROUND-COLOR: #f5f8f0">>      However it
>is worth asking why you wish wish to 'improve' the appearance of your
>images and whether this is ethical. 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-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. STYLE: normal; BACKGROUND-COLOR: #f5f8f0">> Better yet deal
>with the source of the artefacts. normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
>#f5f8f0">> Jeremy Adler FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
>Cell Biology 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">> The
>Wenner-Gren Inst. 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> Arrhenius Laboratories E5 FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
>Stockholm University SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
>Stockholm 106 91 SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
>Sweden 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
>________________________________ WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
>#f5f8f0">> From: Confocal Microscopy List on behalf of
>MODEL, MICHAEL FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">> Sent: Thu
>5/8/2008 16:09 FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">> </
>FONT>To: <A href="java_script:main.compose
>('new','t=[hidden email]')"
>target="1">[hidden email]</A> 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> 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">> Dear
>List - 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. 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
>Michael Model, Ph.D. FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
>Confocal Microscopy Core 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 WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
>#f5f8f0">> tel. 330-672-
>2874 </BLOCKQUOTE> style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;
>BACKGROUND-COLOR: #f5f8f0">> -- WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
>#f5f8f0">> -- SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
>Zoltan Cseresnyes SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
>Facility manager, Imaging Suite normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
>#f5f8f0">>  Dept. of Zoology University of
>Cambridge style="DISPLAY: inline; FONT-WEIGHT: normal; FONT
>-SIZE: medium; COLOR: black; FONT-STYLE: normal; BACKGROUND-COLOR:
>white">
><HR>
> <A href="https://antispam.osu.edu/b.php?
>c=s&i=597223478&m=473bf06adf8d" target=1>WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
>#f5f8f0">> Spam</A> <A
>href="https://antispam.osu.edu/b.php?
>c=n&i=597223478&m=473bf06adf8d" target=1>WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
>#f5f8f0">> Not spam</A> <A
>href="https://antispam.osu.edu/b.php?
>c=f&i=597223478&m=473bf06adf8d" target=1>WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
>#f5f8f0">> 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>
>
>------------------------------
>
>Date: Mon, 12 May 2008 15:35:36 -0400
>From: RICHARD BURRY <[hidden email]>
>Subject: Re: interpolation Note of Caution
>
>This is a multi-part message in MIME format.
>
>----61c70de2795b48832b2b
>Content-Type: text/html; charset=us-ascii
>Content-Disposition: inline
>Content-Transfer-Encoding: quoted-printable
>
>Search the CONFOCAL archive at
>http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=3Dconfocal
>=3CP class=3DMsoNormal=3EThe guidelines Doug posted on the Univ=2E Arizo=
>na website are great=2E=26nbsp=3B One issue that makes digital images mo=
>re suspect=2C is the individual element of the image=2C the pixel=2C can=
> be changed=2E=26nbsp=3B With photographic manipulations we were burning=
> in regions not selectively changing the intensity of a single pixel=2E=26=
>nbsp=3B Most journals today reserve the right to ask authors for the ori=
>ginal image files that were taken on the CCD camera or came from the con=
>focal=2E=26nbsp=3B As listed by Doug in his guidelines=2C it is most imp=
>ortant to retain archive files of ALL original images=2E=26nbsp=3B This =
>allows you to go back to the original if needed=2E=26nbsp=3B =3C=3Fxml=3A=
>namespace prefix =3D o /=3E=3Co=3Ap=3E=3C/o=3Ap=3E=3C/P=3E
>=3CP class=3DMsoNormal=3E=3Co=3Ap=3E=26nbsp=3B=3C/o=3Ap=3EOne mistake th=
>at authors are making in submitted manuscripts is to saturate=26nbsp=3Bt=
>he intense pixels in images=2E=26nbsp=3B The images look almost like lin=
>e drawings and not micrographs=2E=26nbsp=3B 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=2E =3C=
>o=3Ap=3E=3C/o=3Ap=3E=3C/P=3E
>=3CP=3EDick Burry=3CBR=3EOhio State University=3Co=3Ap=3E=3C/o=3Ap=3E=3C=
>/P=3E=3CBR=3E=3CBR=3E----- Original Message -----=3CBR=3EFrom=3A Doug Cr=
>omey =26lt=3Bcromey=40arizona=2Eedu=26gt=3B=3CBR=3EDate=3A Monday=2C May=
> 12=2C 2008 12=3A54 pm=3CBR=3ESubject=3A Re=3A interpolation Note of Cau=
>tion=3CBR=3ETo=3A CONFOCAL=40LISTSERV=2EBUFFALO=2EEDU=3CBR=3E=3CBR=3E=26=
>gt=3B Search the CONFOCAL archive at=3CBR=3E=26gt=3B http=3A//listserv=2E=
>acsu=2Ebuffalo=2Eedu/cgi-bin/wa=3FS1=3Dconfocal=3CBR=3E=26gt=3B =3CBR=3E=
>=26gt=3B I=27ve been thinking about the issue of digital imaging ethics =
>for =3CBR=3E=26gt=3B awhile=2EMuch of what we could get away with in the=
> days of the =3CBR=3E=26gt=3B photographic darkroom=3CBR=3E=26gt=3B woul=
>d no longer be considered appropriate these days=2E=26nbsp=3B The =3CBR=3E=
>=26gt=3B JCB has pretty=3CBR=3E=26gt=3B explicit digital image guideline=
>s=2C I suspect that other journals =3CBR=3E=26gt=3B that are=3CBR=3E=26g=
>t=3B without specific guidelines are probably =22behind the =3CBR=3E=26g=
>t=3B curve=22=2E=26nbsp=3B =3CBR=3E=26gt=3B =3CBR=3E=26gt=3B My take has=
> always been that if you fully describe the steps =3CBR=3E=26gt=3B that =
>are taken=3CBR=3E=26gt=3B in processing an image=2C then no one can accu=
>se you of misconduct (1)=2E=3CBR=3E=26gt=3B Reviewers =26amp=3B Editors =
>may not like your image processing protocol=2C =3CBR=3E=26gt=3B but then=
> it=3CBR=3E=26gt=3B becomes an issue of scientific discussion=2C not an =
>accusation=2E=3CBR=3E=26gt=3B =3CBR=3E=26gt=3B I=27ve proposed some digi=
>tal imaging ethical guidelines here=3A=3CBR=3E=26gt=3B http=3A//swehsc=2E=
>pharmacy=2Earizona=2Eedu/exppath/micro/digimage=5Fethics=2Ehtml=3CBR=3E=26=
>gt=3B =3CBR=3E=26gt=3B Some colleagues at the University of Alabama - Bi=
>rmingham are =3CBR=3E=26gt=3B working on a=3CBR=3E=26gt=3B web site that=
> includes these guidelines and a video case study=2C =3CBR=3E=26gt=3B bu=
>t it=27s not=3CBR=3E=26gt=3B quite done yet=2E=26nbsp=3B I=27ll post the=
> URL when the folks at UAB =3CBR=3E=26gt=3B let me know they=3CBR=3E=26g=
>t=3B are done=2E=3CBR=3E=26gt=3B =3CBR=3E=26gt=3B Doug Cromey=3CBR=3E=26=
>gt=3B =3CBR=3E=26gt=3B =3CBR=3E=26gt=3B (1) The HHS Office of Research I=
>ntegrity officially defines scientific=3CBR=3E=26gt=3B misconduct as=3A=26=
>nbsp=3B =22=2Efabrication=2C falsification=2C or plagiarism =3CBR=3E=26g=
>t=3B in proposing=2C=3CBR=3E=26gt=3B performing=2C or reviewing research=
>=2C or in reporting research results=2E=22=3CBR=3E=26gt=3B =3CBR=3E=26gt=
>=3B * Fabrication is making up data or results and recording or =3CBR=3E=
>=26gt=3B reporting them=2E=3CBR=3E=26gt=3B * Falsification is manipulati=
>ng research materials=2C equipment=2C =3CBR=3E=26gt=3B or processes=2C=3C=
>BR=3E=26gt=3B or changing or omitting data or results such that the rese=
>arch =3CBR=3E=26gt=3B is not=3CBR=3E=26gt=3B accurately represented in t=
>he research record=2E=3CBR=3E=26gt=3B * Plagiarism is the appropriation =
>of another person=27s ideas=2C =3CBR=3E=26gt=3B processes=2Cresults=2C o=
>r words without giving appropriate credit=2E=3CBR=3E=26gt=3B * Research =
>misconduct does not include differences of opinion=2E=3CBR=3E=26gt=3B =3C=
>BR=3E=26gt=3B FROM=3A=26nbsp=3B http=3A//ori=2Ehhs=2Egov/publications/or=
>i=5Fintro=5Ftext=2Eshtml=3CBR=3E=26gt=3B =3CBR=3E=26gt=3B =5E=5E=5E=5E=5E=
>=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=
>=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=5E=
>=5E=5E=5E=5E=5E=5E=3CBR=3E=26gt=3B Douglas W=2E Cromey=2C M=2ES=2E - Ass=
>istant Scientific Investigator=3CBR=3E=26gt=3B Dept=2E of Cell Biology =26=
>amp=3B Anatomy=2C University of Arizona=3CBR=3E=26gt=3B 1501 N=2E Campbe=
>ll Ave=2C Tucson=2C AZ=26nbsp=3B 85724-5044 USA=3CBR=3E=26gt=3B =3CBR=3E=
>=26gt=3B office=3A=26nbsp=3B AHSC =3CBR=3E=26gt=3B 4212=26nbsp=3B=26nbsp=
>=3B=26nbsp=3B=26nbsp=3B=26nbsp=3B=26nbsp=3B=26nbsp=3B=26nbsp=3B email=3A=
> =3CBR=3E=26gt=3B Cromey=40Arizona=2Eeduvoice=3A=26nbsp=3B 520-626-=3CBR=
>=3E=26gt=3B 2824=26nbsp=3B=26nbsp=3B=26nbsp=3B=26nbsp=3B=26nbsp=3B=26nbs=
>p=3B fax=3A=26nbsp=3B 520-626-2097=3CBR=3E=26gt=3B =3CBR=3E=26gt=3B http=
>=3A//swehsc=2Epharmacy=2Earizona=2Eedu/exppath/=3CBR=3E=26gt=3B Home of=3A=
> =22Microscopy and Imaging Resources on the WWW=22=3CBR=3E=26gt=3B =3CBR=
>=3E=26gt=3B =3CBR=3E=26gt=3B -----Original Message-----=3CBR=3E=26gt=3B =
>From=3A Confocal Microscopy List =3CBR=3E=26gt=3B =5Bmailto=3ACONFOCAL=40=
>LISTSERV=2EBUFFALO=2EEDU=5D On=3CBR=3E=26gt=3B Behalf Of MODEL=2C MICHAE=
>L=3CBR=3E=26gt=3B Sent=3A Friday=2C May 09=2C 2008 7=3A43 AM=3CBR=3E=26g=
>t=3B To=3A CONFOCAL=40LISTSERV=2EBUFFALO=2EEDU=3CBR=3E=26gt=3B Subject=3A=
> Re=3A interpolation Note of Caution=3CBR=3E=26gt=3B =3CBR=3E=26gt=3B Se=
>arch the CONFOCAL archive at=3CBR=3E=26gt=3B http=3A//listserv=2Eacsu=2E=
>buffalo=2Eedu/cgi-bin/wa=3FS1=3Dconfocal=3CBR=3E=26gt=3B =3CBR=3E=26gt=3B=
> I certainly didn=27t=27 expect to start a big discussion of this =3CBR=3E=
>=26gt=3B topic=2E I=3CBR=3E=26gt=3B agree that the Notes of Caution are =
>fully justified=2E On the =3CBR=3E=26gt=3B other hand=2C=3CBR=3E=26gt=3B=
> in Russ=27 Image Processing Handbook you will find many examples =3CBR=3E=
>=26gt=3B of very=3CBR=3E=26gt=3B drastic editing of microscopic images=2C=
> so in some situations it =3CBR=3E=26gt=3B must be=3CBR=3E=26gt=3B accep=
>table=2E Is it up to each journal to set up their own =3CBR=3E=26gt=3B g=
>uidelines=3F It=3CBR=3E=26gt=3B seems to me that so long as the author f=
>ully explained what had been=3CBR=3E=26gt=3B done to the images it=27s n=
>ot cheating=2C but I may be wrong=2E (I =3CBR=3E=26gt=3B think we=3CBR=3E=
>=26gt=3B already had this discussion on this forum before)=2E =3CBR=3E=26=
>gt=3B =3CBR=3E=26gt=3B -----Original Message-----=3CBR=3E=26gt=3B From=3A=
> Confocal Microscopy List =3CBR=3E=26gt=3B =5Bmailto=3ACONFOCAL=40LISTSE=
>RV=2EBUFFALO=2EEDU=5D On=3CBR=3E=26gt=3B Behalf Of Eric Scarfone=3CBR=3E=
>=26gt=3B Sent=3A Friday=2C May 09=2C 2008 9=3A46 AM=3CBR=3E=26gt=3B To=3A=
> CONFOCAL=40LISTSERV=2EBUFFALO=2EEDU=3CBR=3E=26gt=3B Subject=3A Re=3A in=
>terpolation Note of Caution=3CBR=3E=26gt=3B =3CBR=3E=26gt=3B Search the =
>CONFOCAL archive at=3CBR=3E=26gt=3B http=3A//listserv=2Eacsu=2Ebuffalo=2E=
>edu/cgi-bin/wa=3FS1=3Dconfocal=3CBR=3E=26gt=3B =3CBR=3E=26gt=3B Hello al=
>l=3CBR=3E=26gt=3B this problem certainly deserves a whole thread (it pro=
>bably has =3CBR=3E=26gt=3B been =3CBR=3E=26gt=3B on this list before=3F)=
>=2E=3CBR=3E=26gt=3B I wonder how one should consider techniques such as =
>background =3CBR=3E=26gt=3B subtraction that have been in use in video-m=
>icroscopy even =3CBR=3E=26gt=3B before the =3CBR=3E=26gt=3B digital age!=
>=3CBR=3E=26gt=3B Isn=27t it also manipulation=3F=3CBR=3E=26gt=3B Eric=3C=
>BR=3E=26gt=3B =3CBR=3E=26gt=3B Eric Scarfone=2C PhD=2C CNRS=2C=3CBR=3E=26=
>gt=3B Center for Hearing and communication Research=3CBR=3E=26gt=3B Depa=
>rtment of Clinical Neuroscience=3CBR=3E=26gt=3B Karolinska Institutet=3C=
>BR=3E=26gt=3B =3CBR=3E=26gt=3B Postal Address=3A=3CBR=3E=26gt=3B CFH=2C =
>M1=3A02=3CBR=3E=26gt=3B Karolinska Hospital=2C=3CBR=3E=26gt=3B SE-171 76=
> Stockholm=2C Sweden=3CBR=3E=26gt=3B =3CBR=3E=26gt=3B Work=3A=26nbsp=3B =
>+46 (0)8-517 79343=2C=3CBR=3E=26gt=3B Cell=3A=26nbsp=3B +46 (0)70 888 23=
>52=3CBR=3E=26gt=3B Fax=3A=26nbsp=3B=26nbsp=3B +46 (0)8-301876=3CBR=3E=26=
>gt=3B =3CBR=3E=26gt=3B email=3A=26nbsp=3B eric=2Escarfone=40ki=2Ese=3CBR=
>=3E=26gt=3B http=3A//www=2Eki=2Ese/cfh/=3CBR=3E=26gt=3B =3CBR=3E=26gt=3B=
> =3CBR=3E=26gt=3B ----- Original Message -----=3CBR=3E=26gt=3B From=3A R=
>ICHARD BURRY =26lt=3Bburry=2E1=40OSU=2EEDU=26gt=3B=3CBR=3E=26gt=3B Date=3A=
> Friday=2C May 9=2C 2008 3=3A28 pm=3CBR=3E=26gt=3B Subject=3A Re=3A inte=
>rpolation Note of Caution=3CBR=3E=26gt=3B To=3A CONFOCAL=40LISTSERV=2EBU=
>FFALO=2EEDU=3CBR=3E=26gt=3B =3CBR=3E=26gt=3B Search the CONFOCAL archive=
> at=3CBR=3E=26gt=3B http=3A//listserv=2Eacsu=2Ebuffalo=2Eedu/cgi-bin/wa=3F=
>S1=3Dconfocal=3CBR=3E=26gt=3B =26lt=3BP class=3DMsoNormal style=3D=22MAR=
>GIN=3A 0in 0in 0pt=22=26gt=3B=26lt=3BFONT =3CBR=3E=26gt=3B face=3D=22Tim=
>es New =3CBR=3E=26gt=3B Roman=22=26gt=3B=26lt=3BFONT size=3D4=26gt=3BThe=
>re are ethical limits as to what is =3CBR=3E=26gt=3B allowed in =3CBR=3E=
>=26gt=3B manipulating micrographs=2E=26lt=3BSPAN style=3D=22mso-spacerun=
>=3A =3CBR=3E=26gt=3B yes=22=26gt=3B=26nbsp=3B =3CBR=3E=26gt=3B =26lt=3B/=
>SPAN=26gt=3BRemoving small unwanted objects is no different than =3CBR=3E=
>=26gt=3B adding =3CBR=3E=26gt=3B small wanted objects=2E=26lt=3BSPAN sty=
>le=3D=22mso-spacerun=3A yes=22=26gt=3B=26nbsp=3B =3CBR=3E=26gt=3B =26lt=3B=
>/SPAN=26gt=3BA =3CBR=3E=26gt=3B great summary with examples is found in =
>a Journal of Cell =3CBR=3E=26gt=3B Biology =3CBR=3E=26gt=3B article by R=
>ossner and Yamada 2004 166=3A11-15 with the pdf =3CBR=3E=26gt=3B availab=
>le at =3CBR=3E=26gt=3B http=3A//www=2Ejcb=2Eorg/cgi/reprint/166/1/11=2E=26=
>lt=3BSPAN style=3D=22mso-=3CBR=3E=26gt=3B spacerun=3A =3CBR=3E=26gt=3B y=
>es=22=26gt=3B=26nbsp=3B =26lt=3B/SPAN=26gt=3BJournal editors are looking=
> for these =3CBR=3E=26gt=3B modifications =3CBR=3E=26gt=3B because autho=
>rs are misrepresentating their =3CBR=3E=26gt=3B data!=26lt=3B=3Fxml=3Ana=
>mespace =3CBR=3E=26gt=3B prefix =3D o ns =3D =22urn=3Aschemas-microsoft-=
>=3CBR=3E=26gt=3B com=3Aoffice=3Aoffice=22 /=26gt=3B=26lt=3Bo=3Ap=26gt=3B=
>=26lt=3B/o=3Ap=26gt=3B=26lt=3B/FONT=26gt=3B=26lt=3B/FONT=26gt=3B=26lt=3B=
>/P=26gt=3B=3CBR=3E=26gt=3B =26lt=3BP=26gt=3B=26lt=3BFONT size=3D4=26gt=3B=
>Dick Burry=26lt=3BBR=26gt=3BOhio State =3CBR=3E=26gt=3B University=26lt=3B=
>BR=26gt=3B=26lt=3B/FONT=26gt=3B=26lt=3BBR=26gt=3B-----=3CBR=3E=26gt=3B =26=
>nbsp=3BOriginal Message -----=26lt=3BBR=26gt=3BFrom=3A Zoltan Cseresnyes=
> =3CBR=3E=26gt=3B =26lt=3Bzcseresn=40GMAIL=2ECOM=26gt=3B=26lt=3BBR=26gt=3B=
>Date=3A Friday=2C May 9=2C 2008 8=3A33 =3CBR=3E=26gt=3B am=26lt=3BBR=26g=
>t=3BSubject=3A Re=3A interpolation Note of Caution=26lt=3BBR=26gt=3BTo=3A=
> =3CBR=3E=26gt=3B CONFOCAL=40LISTSERV=2EBUFFALO=2EEDU=26lt=3BBR=26gt=3B=26=
>lt=3BBR=26gt=3B=26lt=3BFONT style=3D=22FONT-=3CBR=3E=26gt=3B WEIGHT=3A n=
>ormal=3B =3CBR=3E=26gt=3B FONT-SIZE=3A 14px=3B FONT-STYLE=3A normal=3B B=
>ACKGROUND-COLOR=3A =3CBR=3E=26gt=3B =23f5f8f0=22=26gt=3B=26gt=3B =3CBR=3E=
>=26gt=3B =26lt=3B/FONT=26gt=3BSearch the CONFOCAL archive at =3CBR=3E=26=
>gt=3B http=3A//listserv=2Eacsu=2Ebuffalo=2Eedu/cgi-bin/wa=3FS1=3Dconfoca=
>l =3CBR=3E=26gt=3B =26lt=3B/P=26gt=3BI=27m =3CBR=3E=26gt=3B completely w=
>ith Jeremy on this subject=2C I don=27t think =3CBR=3E=26gt=3B it=27s=26=
>nbsp=3Bgood =3CBR=3E=26gt=3B practice=26nbsp=3Bto remove parts of your i=
>mage just for its own =3CBR=3E=26gt=3B sake=2E=26nbsp=3B You can e=2Eg=2E=
> false-colour the real or the artificial =3CBR=3E=26gt=3B pixels=2C in o=
>rder to show the readers which objects to pay =3CBR=3E=26gt=3B attention=
> =3CBR=3E=26gt=3B to=2E=26nbsp=3B Just my 2c of course=2E=26lt=3BBR=26gt=
>=3B=26nbsp=3B=26lt=3BBR=26gt=3B=26lt=3BFONT =3CBR=3E=26gt=3B style=3D=22=
>FONT-WEIGHT=3A =3CBR=3E=26gt=3B normal=3B FONT-SIZE=3A 14px=3B FONT-STYL=
>E=3A normal=3B BACKGROUND-COLOR=3A =3CBR=3E=26gt=3B =23f5f8f0=22=26gt=3B=
>=26gt=3B =26lt=3B/FONT=26gt=3BZoltan=26lt=3BBR=26gt=3B=26lt=3BBR=26gt=3B=
>=26lt=3BBR=26gt=3B=3CBR=3E=26gt=3B =26lt=3BDIV class=3Dgmail=5Fquote=26g=
>t=3B=26lt=3BFONT style=3D=22FONT-WEIGHT=3A normal=3B =3CBR=3E=26gt=3B FO=
>NT-SIZE=3A =3CBR=3E=26gt=3B 14px=3B FONT-STYLE=3A normal=3B BACKGROUND-C=
>OLOR=3A =23f5f8f0=22=26gt=3B=26gt=3B =3CBR=3E=26gt=3B =26lt=3B/FONT=26gt=
>=3BOn =3CBR=3E=26gt=3B Fri=2C May 9=2C 2008 at 8=3A37 AM=2C Jeremy Adler=
> =26lt=3B=26lt=3BA =3CBR=3E=26gt=3B href=3D=22java=5Fscript=3Amain=2Ecom=
>pose(=27new=27=2C=27t=3Dadler=2Ejeremy=40cellbio=2Esu=2Ese=27)=22 =3CBR=3E=
>=26gt=3B target=3D=221=22=26gt=3Badler=2Ejeremy=40cellbio=2Esu=2Ese=26lt=
>=3B/A=26gt=3B=26gt=3B wrote=3A=26lt=3BBR=26gt=3B=3CBR=3E=26gt=3B =26lt=3B=
>BLOCKQUOTE class=3Dgmail=5Fquote style=3D=22PADDING-LEFT=3A 1ex=3B =3CBR=
>=3E=26gt=3B MARGIN=3A 0px =3CBR=3E=26gt=3B 0px 0px 0=2E8ex=3B BORDER-LEF=
>T=3A =23ccc 1px solid=22=26gt=3B=26lt=3BFONT style=3D=22FONT-=3CBR=3E=26=
>gt=3B WEIGHT=3A =3CBR=3E=26gt=3B normal=3B FONT-SIZE=3A 14px=3B FONT-STY=
>LE=3A normal=3B BACKGROUND-COLOR=3A =3CBR=3E=26gt=3B =23f5f8f0=22=26gt=3B=
>=26gt=3B =26lt=3B/FONT=26gt=3BSearch the CONFOCAL archive =3CBR=3E=26gt=3B=
> at=26lt=3BBR=26gt=3B=26lt=3BA =3CBR=3E=26gt=3B href=3D=22http=3A//lists=
>erv=2Eacsu=2Ebuffalo=2Eedu/cgi-bin/wa=3FS1=3Dconfocal=22 =3CBR=3E=26gt=3B=
> target=3D1=26gt=3B=26lt=3BFONT style=3D=22FONT-WEIGHT=3A normal=3B FONT=
>-SIZE=3A 14px=3B =3CBR=3E=26gt=3B FONT-=3CBR=3E=26gt=3B STYLE=3A normal=3B=
> BACKGROUND-COLOR=3A =23f5f8f0=22=26gt=3B=26gt=3B =3CBR=3E=26gt=3B =26lt=
>=3B/FONT=26gt=3Bhttp=3A//listserv=2Eacsu=2Ebuffalo=2Eedu/cgi-bin/wa=3F=3C=
>BR=3E=26gt=3B S1=3Dconfocal=26lt=3B/A=26gt=3B=26lt=3BBR=26gt=3B=26lt=3BB=
>R=26gt=3B=26lt=3BFONT style=3D=22FONT-WEIGHT=3A =3CBR=3E=26gt=3B normal=3B=
> FONT-SIZE=3A =3CBR=3E=26gt=3B 14px=3B FONT-STYLE=3A normal=3B BACKGROUN=
>D-COLOR=3A =23f5f8f0=22=26gt=3B=26gt=3B =3CBR=3E=26gt=3B =26lt=3B/FONT=26=
>gt=3BRemoval of artefacts=2E=26lt=3BBR=26gt=3B=26lt=3BBR=26gt=3B=26lt=3B=
>FONT =3CBR=3E=26gt=3B style=3D=22FONT-WEIGHT=3A normal=3B =3CBR=3E=26gt=3B=
> FONT-SIZE=3A 14px=3B FONT-STYLE=3A normal=3B BACKGROUND-COLOR=3A =3CBR=3E=
>=26gt=3B =23f5f8f0=22=26gt=3B=26gt=3B =3CBR=3E=26gt=3B =26lt=3B/FONT=26g=
>t=3B1) Smooth your artefact free image=2C and use the mask =3CBR=3E=26gt=
>=3B to select =3CBR=3E=26gt=3B the areas from the smoothed image that yo=
>u wish to insert into =3CBR=3E=26gt=3B the =3CBR=3E=26gt=3B original=2E =
>Only fiddle the problematic pixels=2E This will only =3CBR=3E=26gt=3B wo=
>rk for =3CBR=3E=26gt=3B small artefacts=2E=26lt=3BBR=26gt=3B=26lt=3BBR=26=
>gt=3B=26lt=3BBR=26gt=3B=26lt=3BBR=26gt=3B=3CBR=3E=26gt=3B =26lt=3BFONT s=
>tyle=3D=22FONT-WEIGHT=3A normal=3B FONT-SIZE=3A 14px=3B FONT-=3CBR=3E=26=
>gt=3B STYLE=3A normal=3B =3CBR=3E=26gt=3B BACKGROUND-COLOR=3A =23f5f8f0=22=
>=26gt=3B=26gt=3B =26lt=3B/FONT=26gt=3B=26nbsp=3B =26nbsp=3B =3CBR=3E=26g=
>t=3B =26nbsp=3BHowever it =3CBR=3E=26gt=3B is worth asking why you wish =
>wish to =27improve=27 the appearance of =3CBR=3E=26gt=3B your =3CBR=3E=26=
>gt=3B images and whether this is ethical=2E=26lt=3BBR=26gt=3B=26lt=3BFON=
>T style=3D=22FONT-=3CBR=3E=26gt=3B WEIGHT=3A =3CBR=3E=26gt=3B normal=3B =
>FONT-SIZE=3A 14px=3B FONT-STYLE=3A normal=3B BACKGROUND-COLOR=3A =3CBR=3E=
>=26gt=3B =23f5f8f0=22=26gt=3B=26gt=3B =26lt=3B/FONT=26gt=3B=26nbsp=3B =26=
>nbsp=3B At the very least a full =3CBR=3E=26gt=3B description of why and=
> how the published image differs from the =3CBR=3E=26gt=3B original imag=
>e must be given=2E=26lt=3BBR=26gt=3B=26lt=3BFONT style=3D=22FONT-WEIGHT=3A=
> =3CBR=3E=26gt=3B normal=3B =3CBR=3E=26gt=3B FONT-SIZE=3A 14px=3B FONT-S=
>TYLE=3A normal=3B BACKGROUND-COLOR=3A =3CBR=3E=26gt=3B =23f5f8f0=22=26gt=
>=3B=26gt=3B =3CBR=3E=26gt=3B =26lt=3B/FONT=26gt=3B=26nbsp=3B =26nbsp=3B =
>From your description you appear able to =3CBR=3E=26gt=3B decide =3CBR=3E=
>=26gt=3B that some features are artefacts and define these features =3CB=
>R=3E=26gt=3B sufficiently well to accurately generate a mask=2E =26nbsp=3B=
>If we =3CBR=3E=26gt=3B assume =3CBR=3E=26gt=3B that the artefects simply=
> obliterate any underlying signal then =3CBR=3E=26gt=3B you =3CBR=3E=26g=
>t=3B have no knowledge of what might have been found in those pixels=2E =
>=3CBR=3E=26gt=3B And =3CBR=3E=26gt=3B no legitimate basis for =27improvi=
>ng=27 your image=2E=26lt=3BBR=26gt=3B=26lt=3BBR=26gt=3B=26lt=3BFO=3CBR=3E=
>=26gt=3B NT style=3D=22FONT-WEIGHT=3A normal=3B FONT-SIZE=3A 14px=3B FON=
>T-STYLE=3A =3CBR=3E=26gt=3B normal=3B =3CBR=3E=26gt=3B BACKGROUND-COLOR=3A=
> =23f5f8f0=22=26gt=3B=26gt=3B =26lt=3B/FONT=26gt=3B=26nbsp=3B =26nbsp=3B=
>Zapping =3CBR=3E=26gt=3B the =3CBR=3E=26gt=3B artefacts and leaving clea=
>r and obvious blanks would be more =3CBR=3E=26gt=3B legitimate than =27i=
>mproving=27 the original=2C but I would strongly =3CBR=3E=26gt=3B favour=
> =3CBR=3E=26gt=3B publishing the originals and explaining/highlighting t=
>he =3CBR=3E=26gt=3B artefacts=2E=26lt=3BBR=26gt=3B=26lt=3BFONT style=3D=22=
>FONT-WEIGHT=3A normal=3B FONT-SIZE=3A =3CBR=3E=26gt=3B 14px=3B FONT-=3CB=
>R=3E=26gt=3B STYLE=3A normal=3B BACKGROUND-COLOR=3A =23f5f8f0=22=26gt=3B=
>=26gt=3B =26lt=3B/FONT=26gt=3BBetter =3CBR=3E=26gt=3B yet deal =3CBR=3E=26=
>gt=3B with the source of the artefacts=2E=26lt=3BBR=26gt=3B=26lt=3BBR=26=
>gt=3B=26lt=3BFONT =3CBR=3E=26gt=3B style=3D=22FONT-WEIGHT=3A =3CBR=3E=26=
>gt=3B normal=3B FONT-SIZE=3A 14px=3B FONT-STYLE=3A normal=3B BACKGROUND-=
>COLOR=3A =3CBR=3E=26gt=3B =23f5f8f0=22=26gt=3B=26gt=3B =26lt=3B/FONT=26g=
>t=3BJeremy Adler=26lt=3BBR=26gt=3B=26lt=3BFONT style=3D=22FONT-=3CBR=3E=26=
>gt=3B WEIGHT=3A normal=3B =3CBR=3E=26gt=3B FONT-SIZE=3A 14px=3B FONT-STY=
>LE=3A normal=3B BACKGROUND-COLOR=3A =3CBR=3E=26gt=3B =23f5f8f0=22=26gt=3B=
>=26gt=3B =3CBR=3E=26gt=3B =26lt=3B/FONT=26gt=3BCell Biology=26lt=3BBR=26=
>gt=3B=26lt=3BFONT style=3D=22FONT-WEIGHT=3A =3CBR=3E=26gt=3B normal=3B F=
>ONT-SIZE=3A =3CBR=3E=26gt=3B 14px=3B FONT-STYLE=3A normal=3B BACKGROUND-=
>COLOR=3A =23f5f8f0=22=26gt=3B=26gt=3B =3CBR=3E=26gt=3B =26lt=3B/FONT=26g=
>t=3BThe =3CBR=3E=26gt=3B Wenner-Gren Inst=2E=26lt=3BBR=26gt=3B=26lt=3BFO=
>NT style=3D=22FONT-WEIGHT=3A normal=3B =3CBR=3E=26gt=3B FONT-SIZE=3A =3C=
>BR=3E=26gt=3B 14px=3B FONT-STYLE=3A normal=3B BACKGROUND-COLOR=3A =23f5f=
>8f0=22=26gt=3B=26gt=3B=3CBR=3E=26gt=3B =26nbsp=3B=26lt=3B/FONT=26gt=3BAr=
>rhenius Laboratories E5=26lt=3BBR=26gt=3B=26lt=3BFONT =3CBR=3E=26gt=3B s=
>tyle=3D=22FONT-WEIGHT=3A normal=3B =3CBR=3E=26gt=3B FONT-SIZE=3A 14px=3B=
> FONT-STYLE=3A normal=3B BACKGROUND-COLOR=3A =3CBR=3E=26gt=3B =23f5f8f0=22=
>=26gt=3B=26gt=3B =3CBR=3E=26gt=3B =26lt=3B/FONT=26gt=3BStockholm Univers=
>ity=26lt=3BBR=26gt=3B=26lt=3BFONT style=3D=22FONT-=3CBR=3E=26gt=3B WEIGH=
>T=3A normal=3B FONT-=3CBR=3E=26gt=3B SIZE=3A 14px=3B FONT-STYLE=3A norma=
>l=3B BACKGROUND-COLOR=3A =23f5f8f0=22=26gt=3B=26gt=3B =3CBR=3E=26gt=3B =26=
>lt=3B/FONT=26gt=3BStockholm 106 91=26lt=3BBR=26gt=3B=26lt=3BFONT style=3D=
>=22FONT-WEIGHT=3A =3CBR=3E=26gt=3B normal=3B FONT-=3CBR=3E=26gt=3B SIZE=3A=
> 14px=3B FONT-STYLE=3A normal=3B BACKGROUND-COLOR=3A =23f5f8f0=22=26gt=3B=
>=26gt=3B =3CBR=3E=26gt=3B =26lt=3B/FONT=26gt=3BSweden=26lt=3BBR=26gt=3B=26=
>lt=3BBR=26gt=3B=26lt=3BFONT style=3D=22FONT-WEIGHT=3A =3CBR=3E=26gt=3B n=
>ormal=3B FONT-SIZE=3A =3CBR=3E=26gt=3B 14px=3B FONT-STYLE=3A normal=3B B=
>ACKGROUND-COLOR=3A =23f5f8f0=22=26gt=3B=26gt=3B =3CBR=3E=26gt=3B =26lt=3B=
>/FONT=26gt=3B=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=
>=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=26lt=3BBR=26gt=3B=26lt=3BBR=26gt=3B=
>=26lt=3BFONT =3CBR=3E=26gt=3B style=3D=22FONT-=3CBR=3E=26gt=3B WEIGHT=3A=
> normal=3B FONT-SIZE=3A 14px=3B FONT-STYLE=3A normal=3B BACKGROUND-=3CBR=
>=3E=26gt=3B COLOR=3A =3CBR=3E=26gt=3B =23f5f8f0=22=26gt=3B=26gt=3B =26lt=
>=3B/FONT=26gt=3BFrom=3A Confocal Microscopy List on behalf =3CBR=3E=26gt=
>=3B of =3CBR=3E=26gt=3B MODEL=2C MICHAEL=26lt=3BBR=26gt=3B=26lt=3BFONT s=
>tyle=3D=22FONT-WEIGHT=3A normal=3B FONT-=3CBR=3E=26gt=3B SIZE=3A 14px=3B=
> =3CBR=3E=26gt=3B FONT-STYLE=3A normal=3B BACKGROUND-COLOR=3A =23f5f8f0=22=
>=26gt=3B=26gt=3B =3CBR=3E=26gt=3B =26lt=3B/FONT=26gt=3BSent=3A Thu =3CBR=
>=3E=26gt=3B 5/8/2008 16=3A09=26lt=3BBR=26gt=3B=26lt=3BFONT style=3D=22FO=
>NT-WEIGHT=3A normal=3B FONT-=3CBR=3E=26gt=3B SIZE=3A 14px=3B =3CBR=3E=26=
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>from the main image without creating unsightly =3CBR=3E=26gt=3B holes=2E=
> =3CBR=3E=26gt=3B Something like automatic =22healing brush=22 in =3CBR=3E=
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>y and Imaging Facility=2C Director =3CBR=3EThe Ohio State University =3C=
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>
>
>----61c70de2795b48832b2b--
>
>------------------------------
>
>Date: Mon, 12 May 2008 18:57:35 -0400
>From: Chris Tully <[hidden email]>
>Subject: Re: interpolation Note of Caution
>
>------=_Part_3299_8865600.1210633055552
>Content-Type: text/plain; charset=ISO-8859-1
>Content-Transfer-Encoding: 7bit
>Content-Disposition: inline
>
>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
>>
>
>------=_Part_3299_8865600.1210633055552
>Content-Type: text/html; charset=ISO-8859-1
>Content-Transfer-Encoding: 7bit
>Content-Disposition: inline
>
>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 (<a href="http://www.mediacy.com/"
>target="_blank">www.mediacy.com</a>)
>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 <a href="mailto:[hidden email]"
>target="_blank">[hidden email]</a> 240-888-1021 <a
>href="http://www.linkedin.com/in/christully"
>target="_blank">http://www.linkedin.com/in/christully</a> 
>
> <div class="gmail_quote">On Mon, May 12, 2008 at 3:35 PM,
>RICHARD BURRY <<a
>href="mailto:[hidden email]">[hidden email]</a>>
>wrote: <blockquote class="gmail_quote" style="border-left: 1px
>solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left:
>1ex;">
><div class="Ih2E3d">Search the CONFOCAL archive at
><a href="http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal"
>target="_blank">http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal</a>
></div>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. 
><div class="Ih2E3d">
>Dick Burry Ohio State University ----- Original
>Message ----- </div><div class="Ih2E3d">From: Doug Cromey <<a
>href="mailto:[hidden email]"
>target="_blank">[hidden email]</a>> Date: Monday, May 12,
>2008 12:54 pm 
>Subject: Re: interpolation Note of Caution To: <a
>href="mailto:[hidden email]"
>target="_blank">[hidden email]</a> > Search
>the CONFOCAL archive at > <a
>href="http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal"
>target="_blank">http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal</a> 
>> </div><div><div></div><div class="Wj3C7c">> 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: > <a
>href="http://swehsc.pharmacy.arizona.edu/exppath/micro/digimage_ethics.html"
>target="_blank">http://swehsc.pharmacy.arizona.edu/exppath/micro/digimage_ethics.html</a> 
>> > 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:  <a
>href="http://ori.hhs.gov/publications/ori_intro_text.shtml"
>target="_blank">http://ori.hhs.gov/publications/ori_intro_text.shtml</a> 
>> >
>^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >
>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:
> </div></div>> [hidden email]: 
>520-626-<div><div></div><div class="Wj3C7c"> >
>2824       fax: 
>520-626-2097 > > <a
>href="http://swehsc.pharmacy.arizona.edu/exppath/"
>target="_blank">http://swehsc.pharmacy.arizona.edu/exppath/</a> 
>> Home of: "Microscopy and Imaging Resources on the
>WWW" > > > -----Original
>Message----- > From: Confocal Microscopy List >
>[mailto:<a href="mailto:[hidden email]"
>target="_blank">[hidden email]</a>] On 
>> Behalf Of MODEL, MICHAEL > Sent: Friday, May 09, 2008
>7:43 AM > To: <a href="mailto:[hidden email]"
>target="_blank">[hidden email]</a> > Subject:
>Re: interpolation Note of Caution 
>> > Search the CONFOCAL archive at > <a
>href="http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal"
>target="_blank">http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal</a> >
> > 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:<a
>href="mailto:[hidden email]"
>target="_blank">[hidden email]</a>] On 
>> Behalf Of Eric Scarfone > Sent: Friday, May 09, 2008 9:46
>AM > To: <a href="mailto:[hidden email]"
>target="_blank">[hidden email]</a> > Subject:
>Re: interpolation Note of Caution 
>> > Search the CONFOCAL archive at > <a
>href="http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal"
>target="_blank">http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal</a> >
> > 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: 
><a href="mailto:[hidden email]"
>target="_blank">[hidden email]</a> > <a
>href="http://www.ki.se/cfh/"
>target="_blank">http://www.ki.se/cfh/</a> > 
>> > ----- Original Message ----- > From: RICHARD
>BURRY <<a href="mailto:[hidden email]"
>target="_blank">[hidden email]</a>> > Date: Friday, May 9,
>2008 3:28 pm > Subject: Re: interpolation Note of Caution 
>> To: <a href="mailto:[hidden email]"
>target="_blank">[hidden email]</a> > >
>Search the CONFOCAL archive at > <a
>href="http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal"
>target="_blank">http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal</a> 
>> 0pt">> face="Times New >
>Roman">There are ethical limits as to
>what is > allowed in > manipulating
>micrographs.
>> yes">  </div></div><div class="Ih2E3d">>
>Removing small unwanted objects is no different than
> > adding > small wanted objects.style="mso-spacerun: yes">  
></div><div class="Ih2E3d">> 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 
>> <a href="http://www.jcb.org/cgi/reprint/166/1/11"
>target="_blank">http://www.jcb.org/cgi/reprint/166/1/11</a>.style="mso- > spacerun: </div>>
>yes">  Journal editors are looking for
>these 
><div class="Ih2E3d">> 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
> </div>> <<a href="mailto:[hidden email]"
>target="_blank">[hidden email]</a>> Date: Friday,
>May 9, 2008 8:33 
><div class="Ih2E3d">> am Subject: Re: interpolation Note
>of Caution To: > <a
>href="mailto:[hidden email]"
>target="_blank">[hidden email]</a> style="FONT- 
>> WEIGHT: normal; > FONT-SIZE: 14px; FONT-STYLE: normal;
>BACKGROUND-COLOR: > #f5f8f0">> </div><div
>class="Ih2E3d">> Search the CONFOCAL archive at
> > <a
>href="http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal"
>target="_blank">http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal</a>
> 
>> I'm > completely with Jeremy on this
>subject, I don't think </div>> 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 
><div class="Ih2E3d">> pixels, in order to show the readers which
>objects to pay > attention </div>> to.  Just my
>2c of course.   <div
>class="Ih2E3d">> style="FONT-WEIGHT: 
>> normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> </div>> #f5f8f0">>
>Zoltan <div
>class="Ih2E3d"> > <DIV class=gmail_quote>style="FONT-WEIGHT: normal; 
>> FONT-SIZE: > 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
>#f5f8f0">> </div>> On > Fri,
>May 9, 2008 at 8:37 AM, Jeremy Adler <<A <div
>class="Ih2E3d">>
>href="java_script:main.compose('new','t=[hidden email]')"
> 
></div>> target="1"><a
>href="mailto:[hidden email]"
>target="_blank">[hidden email]</a></A>>
>wrote: <div class="Ih2E3d"> > <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:
> </div>> #f5f8f0">> Search the
>CONFOCAL archive 
><div class="Ih2E3d">> at <A > href="<a
>href="http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal"
>target="_blank">http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal</a>"
> > target=1>FONT-SIZE: 14px; 
>> FONT- > STYLE: normal; BACKGROUND-COLOR:
>#f5f8f0">> </div><div class="Ih2E3d">>
><a href="http://listserv.acsu.buffalo.edu/cgi-bin/wa"
>target="_blank">http://listserv.acsu.buffalo.edu/cgi-bin/wa</a>? 
>> S1=confocal</A> style="FONT-WEIGHT: > normal; FONT-SIZE: > 14px;
>FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> </div><div class="Ih2E3d">> Removal of
>artefacts. 
>> style="FONT-WEIGHT: normal; > FONT-SIZE: 14px;
>FONT-STYLE: normal; BACKGROUND-COLOR: > #f5f8f0">>
> </div><div class="Ih2E3d">> 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: normal; </div>> BACKGROUND-COLOR:
>#f5f8f0">>     <div
>class="Ih2E3d">>  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: </div>> #f5f8f0">>
>    At the very least a full 
><div class="Ih2E3d">> 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">> </div>>    
>From your description you appear able to <div
>class="Ih2E3d">> decide > that some features are artefacts
>and define these features </div>> sufficiently well to
>accurately generate a mask.  If we 
><div class="Ih2E3d">> 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; </div>> BACKGROUND-COLOR:
>#f5f8f0">>    Zapping <div
>class="Ih2E3d">> 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. style="FONT-WEIGHT: normal; FONT-SIZE: 
>> 14px; FONT- </div>> STYLE: normal; BACKGROUND-COLOR:
>#f5f8f0">> Better <div
>class="Ih2E3d">> yet deal > with the source of the
>artefacts. >
>style="FONT-WEIGHT: 
>> normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
> </div>> #f5f8f0">> Jeremy
>Adler class="Ih2E3d"> > WEIGHT: normal; > FONT-SIZE: 14px;
>FONT-STYLE: normal; BACKGROUND-COLOR: 
>> #f5f8f0">> </div><div class="Ih2E3d">>
>Cell Biology > normal; FONT-SIZE: > 14px; FONT-STYLE: normal;
>BACKGROUND-COLOR: #f5f8f0">> 
></div><div class="Ih2E3d">> The > Wenner-Gren
>Inst. >
>FONT-SIZE: > 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
>#f5f8f0">> 
></div><div class="Ih2E3d">>  Arrhenius
>Laboratories E5 > style="FONT-WEIGHT:
>normal; > FONT-SIZE: 14px; FONT-STYLE: normal;
>BACKGROUND-COLOR: > #f5f8f0">> 
></div><div class="Ih2E3d">> Stockholm
>University > WEIGHT:
>normal; FONT- > SIZE: 14px; FONT-STYLE: normal;
>BACKGROUND-COLOR: #f5f8f0">> </div>
><div class="Ih2E3d">> Stockholm 106
>91 > normal;
>FONT- > SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR:
>#f5f8f0">> </div><div class="Ih2E3d">
>> Sweden style="FONT-WEIGHT: > normal; FONT-SIZE: > 14px;
>FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> </div><div class="Ih2E3d">>
>________________________________ 
>> style="FONT- > WEIGHT: normal; FONT-SIZE: 14px;
>FONT-STYLE: normal; BACKGROUND- > COLOR: </div>>
>#f5f8f0">> From: Confocal Microscopy List on
>behalf <div class="Ih2E3d">
>> of > MODEL, MICHAEL style="FONT-WEIGHT: normal; FONT- > SIZE: 14px; >
>FONT-STYLE: normal; BACKGROUND-COLOR: #f5f8f0">>
> </div><div class="Ih2E3d">> Sent: Thu 
>> 5/8/2008 16:09 normal; FONT- > SIZE: 14px; </div>> FONT-STYLE: normal;
>BACKGROUND-COLOR: #f5f8f0">> </<div
>class="Ih2E3d"> > FONT>To: <A
>href="java_script:main.compose 
>> ('new','t=[hidden email]')"
> > target="1"><a
>href="mailto:[hidden email]"
>target="_blank">[hidden email]</a></A> 
>> style="FONT- > WEIGHT: normal; FONT-SIZE: 14px;
>FONT-STYLE: normal; BACKGROUND- > COLOR: </div>>
>#f5f8f0">> Subject: <div
>class="Ih2E3d">>
>inetrpolation 
>> style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE:
>normal; </div>> BACKGROUND-COLOR: #f5f8f0">>
>Search the CONFOCAL <div class="Ih2E3d">>
>archive at > <A href="<a
>href="http://listserv.acsu.buffalo.edu/cgi-"
>target="_blank">http://listserv.acsu.buffalo.edu/cgi-</a> 
>> bin/wa?S1=confocal" > target=1><a
>href="http://listserv.acsu.buffalo.edu/cgi-bin/wa"
>target="_blank">http://listserv.acsu.buffalo.edu/cgi-bin/wa</a>? >
>S1=confocal</A> style="FONT-WEIGHT: 
>> normal; FONT-SIZE: > 14px; FONT-STYLE: normal;
>BACKGROUND-COLOR: #f5f8f0">> </div><div
>class="Ih2E3d">> Dear > List
>- style="FONT-WEIGHT: 
>> normal; FONT-SIZE: > 14px; FONT-STYLE: normal;
>BACKGROUND-COLOR: #f5f8f0">> </div><div
>class="Ih2E3d">> 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- </div>> COLOR: #f5f8f0">>
>For instance, a control image may <div
>class="Ih2E3d">> 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. style="FONT- 
>> WEIGHT: normal; FONT-SIZE: > 14px; FONT-STYLE: normal;
>BACKGROUND-COLOR: #f5f8f0">> </div><div
>class="Ih2E3d">> Michael Model,
>Ph.D. 
>> WEIGHT: normal; > FONT-SIZE: 14px; FONT-STYLE: normal;
>BACKGROUND-COLOR: > #f5f8f0">> </div><div
>class="Ih2E3d">> Confocal Microscopy
>Core 
>> style="FONT-WEIGHT: > normal; FONT-SIZE: 14px;
>FONT-STYLE: normal; BACKGROUND-COLOR: </div>>
>#f5f8f0">> Dpt. Biological <div
>class="Ih2E3d">> Sciences style="FONT- 
>> WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;
>BACKGROUND- > COLOR: </div>> #f5f8f0">>
>Kent State <div class="Ih2E3d">>
>University 
>> WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal;
>BACKGROUND-COL </div>> OR: #f5f8f0">>
>Kent, OH 44242 <div
>class="Ih2E3d">> style="FONT- > WEIGHT: normal;
>FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND- 
>> COLOR: </div>> #f5f8f0">> tel.
>330-672-<div class="Ih2E3d"> >
>2874 </BLOCKQUOTE> > clear=all> 
>> style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE:
>normal; </div>> BACKGROUND-COLOR: #f5f8f0">>
>-- <div class="Ih2E3d">>
>style="FONT- > WEIGHT: normal; FONT-SIZE: 14px;
>FONT-STYLE: normal; BACKGROUND- 
>> COLOR: </div>> #f5f8f0">> --
> <div
>class="Ih2E3d">> normal; FONT- > SIZE: 14px; FONT-STYLE:
>normal; BACKGROUND-COLOR: #f5f8f0">> 
></div><div class="Ih2E3d">> Zoltan
>Cseresnyes >
>normal; FONT- > SIZE: 14px; FONT-STYLE: normal;
>BACKGROUND-COLOR: #f5f8f0">> </div><div
>class="Ih2E3d">
>> Facility manager, Imaging Suite > style="FONT-WEIGHT: > normal; FONT-SIZE: 14px;
>FONT-STYLE: normal; BACKGROUND-COLOR: </div>>
>#f5f8f0">>  Dept. of Zoology University
>of 
>> > > -- >
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>END-ANTISPAM-VOTING-LINKS<div class="Ih2E3d"> >
> Richard W. Burry, Ph.D. </div><div
>class="Ih2E3d">Department of Neuroscience, College of Medicine 
></div><div class="Ih2E3d">Campus Microscopy and Imaging Facility,
>Director </div>The Ohio State University <div
>class="Ih2E3d">Associate Editor, Journal of Histochemistry and
>Cytochemistry </div><div><div></div>
><div class="Wj3C7c">3018 Graves Hall 333 West Tenth Avenue
> Columbus, Ohio 43210 Voice 614.292.2814  Cell
>614.638.3345  Fax
>614.688.8742 </div></div></blockquote></div>
>
>------=_Part_3299_8865600.1210633055552--
>
>------------------------------
>
>End of CONFOCAL Digest - 11 May 2008 to 12 May 2008 (#2008-124)
>***************************************************************