ImageJ - Re: Fwd: interpolation Note of Caution

ImageJ

Re: Fwd: interpolation Note of Caution

Posted by Joel Sheffield on May 12, 2008; 11:35pm
URL: http://imagej.273.s1.nabble.com/Fwd-interpolation-Note-of-Caution-tp3696252p3696253.html

Hidden in the plugins menu under "macros" is the option to record.
This will capture most of the operations. It was designed to assist
with macro construction, and It is not designed to be a full audit
trail, but it is a fair beginning. I have been asking my students to
use it as they learn to manipulate and measure images.

Joel

Date sent: Mon, 12 May 2008 19:24:06 -0400
Send reply to: ImageJ Interest Group <[hidden email]>
From: John Oreopoulos <[hidden email]>
Subject: Fwd: interpolation Note of Caution
To: [hidden email]

> There is a very interesting topic discussion regarding image
> manipulation going on at the confocal microscopy listserver (see
> forwarded thread discussion) and I was wondering if someone has
> already created an ImageJ plugin that records what actions have been
> performed on an image or an image stack.
>
> John Oreopoulos
>
> Begin forwarded message:
>
> > From: Chris Tully <[hidden email]>
> > Date: May 12, 2008 6:57:35 PM EDT (CA)
> > To: [hidden email]
> > Subject: Re: interpolation Note of Caution
> > Reply-To: Confocal Microscopy List <[hidden email]>
> >
> > Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-
> > bin/wa?S1=confocal List members,
> >
> > First let me explain that although I am no longer associated with
> > them, I have previously worked for Media Cybernetics.
> >
> > One extremely valuable set of features in Image-Pro Plus
> > (www.mediacy.com) is the Audit Trail and Image or File Signature.
> > The Audit Trail logs every action taken on every open image. This
> > allows you to document exactly what was done with or to the image.
> > The Image and File Signatures are 32 bit check sums that are
> > automatically recorded in the Audit trail at 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
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> > >
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> > >
> >
> > Richard W. Burry, Ph.D.
> > Department of Neuroscience, College of Medicine
> > Campus Microscopy and Imaging Facility, Director
> > The Ohio State University
> > Associate Editor, Journal of Histochemistry and Cytochemistry
> > 3018 Graves Hall
> > 333 West Tenth Avenue
> > Columbus, Ohio 43210
> > Voice 614.292.2814 Cell 614.638.3345 Fax 614.688.8742

Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL: http://astro.temple.edu/~jbs