I totally absolutely with Scott's point wrote. I'd like to suggest that 
a simpler definition of acceptable image manipulation might be: That 
there exists a continuous transfer function between input and output?

Regards Mark Cannell

Turner, Scott wrote:
> While I agree that a certain amount of image processing should be allowed and in fact ought to be expected, the news story reported here actually misrepresents the conclusions of the University of Minnesota's ethics panel.  It is not simply that image brightness and contrast were changed; according to the conclusions of the panel (attached below) there were manipulations of images that could be construed as falsification of data.  These included "elimination of bands on blots, altered orientation of bands, introduction of lanes not included in the original figure, and covering objects or image density in certain lanes."  
>
> I think that we can all agree that processing images is often desirable, and in some cases even necessary.  What should not happen, and according to the University of Minnesota did happen in this case, is the manipulation of images to present data in a way that are not consistent with the original content of the image.  Obviously, eliminating unwanted bands from a blot or altering the orientation of a band or including lanes not in the original figure go beyond image processing into the realm of data manipulation.  While it might be acceptable to brighten an image to make it more legible for print, it is not acceptable to cut and paste bands or lanes in a gel or alter the orientation of a band in order to better represent your data.
>
>
> Scott Turner
> Scientist II
> Schering-Plough Biopharma
> Palo Alto, CA
>
>
>
> Statement from the University of Minnesota
>
> University Misconduct Panel Concludes That Certain Data in Stem Cell Paper Were Falsified
>
> University of Minnesota Vice President for Research Tim Mulcahy has accepted the conclusions of an academic misconduct committee impaneled by the University which found that certain data published in the journal Blood in 2001 in connection with federally sponsored stem cell research at the University were falsified.  The University has asked the journal to retract the article.  Vice President Mulcahy also accepted the findings of discrepancies, but not falsification, in certain data published in the Journal of Clinical Investigation.
>
> Two current or former University employees were the subject of a complaint.  Dr. Catherine Verfaillie was previously a full-time tenured faculty member at the University of Minnesota. Dr. Verfaillie is currently the Director of the Stem Cell Institute at the Catholic University in Leuven, Belgium, and retains a 10 percent faculty appointment at the University of Minnesota. Dr. Morayma Reyes was a University of Minnesota student in the combined M.D./Ph.D. program who worked in Dr. Verfaillie's laboratory. Dr. Reyes is currently an Assistant Professor of Pathology at the University of Washington. None of the co-authors of the papers or other laboratory personnel were subjects of any complaints or findings. 
>
> The complaint was investigated by an investigation committee, chaired by Dr. David Bernlohr, Professor of Biochemistry, Molecular Biology and Biophysics at the University of Minnesota, and included Dr. Karen Reue, Professor of Human Genetics at the David Geffen School of Medicine - UCLA, and Dr. William Smith, Professor of Biological Chemistry at the University of Michigan. The panel was charged with investigating complaints against the respondents pursuant to federal regulation 42 C.F.R. § 93.310 and the University's Academic Misconduct Policy after an earlier inquiry conducted by Senior Administrator Charles Muscoplat concluded that there had been sufficient questions raised about the research to warrant a full investigation.
>
> The investigation panel submitted its final report to the Senior Administrator on September 5, 2008.  The panel concluded that parts of four figures in the Blood paper were falsified.  Allegations against Dr. Verfaillie were unsubstantiated.  The findings with respect to Dr. Reyes are private student data and cannot be released under the Minnesota Government Data Practices Act and the federal Family Educational Rights and Privacy Act (FERPA).
>
> The Senior Administrator accepted the panel's report on September 12, 2008, and forwarded it to the Vice President for Research, Tim Mulcahy, who is the senior University official responsible for oversight of academic misconduct proceedings.  Vice President Mulcahy reviewed the report, accepted the panel's conclusions and issued the University's final decision on September 24, 2008.  On September 25, 2008, Vice President Mulcahy transmitted the investigation panel's report and other required materials to the federal Office for Research Integrity for its review and action as required under federal rules governing research supported by the Public Health Service (PHS).
>
> In four of seven figures in the Blood paper, the panel concluded that aspects of the figures were altered in such a way that the manipulation misrepresented experimental data and sufficiently altered the original research record to constitute falsification under federal regulations and University policy.  Manipulations identified by the panel included: elimination of bands on blots, altered orientation of bands, introduction of lanes not included in the original figure, and covering objects or image density in certain lanes. 
>
> In one case all exposures of the source data for the published image were missing.  While the panel could not conclude misconduct in this case, it concluded that the figure should be withdrawn as it cannot be substantiated by the existing experimental record.  The panel found no academic misconduct in the remaining two figures in the Blood paper.
>
> The panel also considered three duplications of Fluorescent Activated Cells Sorting (FACS) data and incorrect labeling included in the article published in Blood, as well as two duplications of FACS data and incorrect labeling in a 2002 article published in the Journal of Clinical Investigation (JCI).  These latter discrepancies were self-reported to the University and JCI by Dr. Verfaillie prior to the initiation of the University's investigation.  In all cases, the panel concluded that no academic misconduct was associated with these FACS discrepancies.  With respect to the FACS discrepancies in the Blood paper, the panel noted poor scientific method and inadequate training and oversight for this research.  The panel made frequent reference to insufficient oversight throughout the report.
>
> Based on the panel's findings, the University has requested that the article entitled "Purification and Ex Vivo Expansion of Postnatal Human Marrow and Mesodermal Progenitor Cells" published in the November 2001 edition of Blood be retracted.  Similarly, the University has notified the editorial office of the Journal of Clinical Investigation of the panel's findings in relation to the FACS discrepancies identified in the article entitled "Origin of Endothelial Progenitors in Human Post-Natal Bone Marrow" published in 2002.  As the panel did not find evidence of academic misconduct related to these figures, the University has not requested that the JCI paper be retracted.
>
> The investigation panel also considered six discrepancies in two figures (Figures 6 and 10) included in an international patent application filed with the U.S. Patent and Trademark Office (USPTO) in August 2000 and again in a corresponding national stage filing dated August 2002.  While concluding that the figures were seriously flawed and not accurate data, there was insufficient evidence to conclude that misconduct occurred in connection with the patent applications.  Nevertheless, the panel recommended that the University notify the company holding the patent interests of these findings and cooperate with the company in making any appropriate disclosures to the USPTO.
>
> The published version of Dr. Reyes' thesis contained all seven western blot discrepancies and three sets of FACS duplications included in the Blood paper.  The University's Student Conduct Code prohibits scholastic dishonesty and falsification in academic work. Student disciplinary proceedings are private, and information about student discipline can be released only in accordance with the Minnesota Government Data Practices Act and FERPA.
>  
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[log in to unmask]] On Behalf Of Johan Henriksson
> Sent: Wednesday, October 08, 2008 11:41 PM
> To: [log in to unmask]
> Subject: Re: An alarming amount of image manipulation - time to fight back
>
> [log in to unmask] wrote:
>   
>> On Wed, 8 Oct 2008, John Oreopoulos wrote:
>>
>>     
>>> My apologies again if this discussion thread becomes heated. I 
>>> thought I'd pass on another news bit about image manipulation, this 
>>> time revolving around brightness and contrast:
>>>
>>> http://www.ctv.ca/servlet/ArticleNews/story/CTVNews/20081008/stemcell
>>> _study_081008/20081008?hub=Health
>>>
>>>
>>> Is this not something the journal should specify and the reviewers 
>>> should be looking for in the first place? It seems to me again that 
>>> all of this could be avoided if the authors simply state and describe 
>>> all image manipulations when submitting for publication
>>>
>>> John Oreopoulos
>>>
>>>       
>> From the story you reference, the researcher did some minimal image 
>> processing that in no way altered the conclusions of the paper, and 
>> was hit on a religious objection that has no practical basis.  Doesn't 
>> sound to clever to me.
>>
>> The position these purists are taking is simply silly.  Were the same 
>> criteria in place before digital imaging, it would be "unethical" to 
>> produce prints from negatives -- or for that matter to even *develop* 
>> negatives at all -- since  all development and all printing
>> *necessarily* involve "image processing."  When was the last time you 
>> created a print without affecting contrast and brightness?  Never?
>> Hmmm....
>>     
> by this logic, the only "ethical" way to include images would be as a table of sensor readouts in the supplementary material. I wonder who would be happy about that.
>
> my stand point here is firm, any image manipulation is allowed. it is better by *default* to assume image processing. but the original image should always be made available in that case. the method description should come in form of a script to redo the operation using an open source package. I think this is how biologists should work with their data anyway because it allows them to redo the operation very easily on other images. as an additional advantage, checking correctedness can be almost automatic, the journal simply reruns the script. the only thing left to argue about is the choice of operations, left to the reviewers.
>
> currently we have too many black boxes; deconvolution operations is one group of very important but hard to describe algorithms (the number of biologists here who has implemented it, raise your hand). I would not in any way be satisfied with a method description "was deconvolved with XXX" because I most likely do not have the package. you cannot expect a reviewer to suddenly shell out 10k usd just to verify a picture.
>
> /Johan
>
> --
> --
> ------------------------------------------------
> Johan Henriksson
> MSc Engineering
> PhD student, Karolinska Institutet
> http://mahogny.areta.org http://www.endrov.net
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