image manipulation
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Dear list I remember hearing or reading somewhere of a Fiji (maybe) plugin to help group leaders detect potential image manipulation but I cannot find what it was. Has anyone heard of it who could point me to the right direction? Med vänlig hälsning / Best regards Sylvie @@@@@@@@@@@@@@@@@@@@@@@@ Sylvie Le Guyader, PhD Live Cell Imaging Facility Manager Karolinska Institutet- Bionut Dpt Blickagången 16, Room 7362 (lab)/7840 (office) 14157 Huddinge, Sweden mobile: +46 (0) 73 733 5008 LCI website<https://ki.se/en/bionut/welcome-to-the-lci-facility> Follow our microscopy blog!<http://microscopykarolinska.se/> När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI's processing of personal data here<https://ki.se/en/staff/data-protection-policy>. |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Dear Sylvie, perhaps you mean InspectJ? Mit vänliga hälsningar, Mika |
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In reply to this post by Sylvie Le Guyader
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Hi Sylvie, You'll hear from many others, and in particular, I'd listen carefully to anything Doug Cromey has to say. From my research, (and I lectured on this matter for a number of years at UVA and around the US) programs developed to detect image manipulation have never been trustworthy and cannot replace human assessment. I realize you've asked only to be "pointed" to the possibility, but I'd strongly suggest avoiding that route if possible and leaning on tools found at the ORI (Office of Research Integrity) and on Doug Cromey's digital image ethics website. I'm sure a good conversation will develop here and you'll come to your own conclusions, but I do think you'll save time by developing your own departmental guidelines for microbiology, and having a screening process for published papers in your department. You might also refer here. Warm regards,Kirsten Digital Image Ethics | The Microscopy Alliance | The University of Arizona 1) Scientific digital images are data that can be compromised by inappropriate manipulations. microscopy.arizona.edu https://ori.hhs.gov/education/products/RIandImages/default.html On Tue, Feb 16, 2021 at 9:36 AM Sylvie Le Guyader <[hidden email]> wrote: ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Dear list I remember hearing or reading somewhere of a Fiji (maybe) plugin to help group leaders detect potential image manipulation but I cannot find what it was. Has anyone heard of it who could point me to the right direction? Med vänlig hälsning / Best regards Sylvie @@@@@@@@@@@@@@@@@@@@@@@@ Sylvie Le Guyader, PhD Live Cell Imaging Facility Manager Karolinska Institutet- Bionut Dpt Blickagången 16, Room 7362 (lab)/7840 (office) 14157 Huddinge, Sweden mobile: +46 (0) 73 733 5008 LCI website<https://ki.se/en/bionut/welcome-to-the-lci-facility> Follow our microscopy blog!<http://microscopykarolinska.se/> När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI's processing of personal data here< https://ki.se/en/staff/data-protection-policy>. |
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In reply to this post by Sylvie Le Guyader
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Hej Sylvie, 1) look at the histogram for each channel 2) use a variance filter - if bits have been cut and pasted from different original images, the variance in the background may differ. 3) a more sophisticated option is to look for the local poisson noise - this should be the same in all areas of the image with a similar intensity - but will differ if cutting and pasting has been used. However there is a competition between those committing fraud and those chasing fraud - both improve. There is also a major interest in comparing papers to check if the same image has been re used. Jeremy =============================================== B i o V i s P l a t f o r m of Uppsala University Light & EM microscopy / FlowCytometry & Cell Sorting / Image Analysis =============================================== Jeremy Adler PhD - Senior research engineer Light, Confocal Microscopy, Image Analysis E-mail: [hidden email] 070-1679349 Dag Hammarskjölds v 20 751 85 UPPSALA, SWEDEN http://biovis.uu.se/ =============================================== -----Original Message----- From: Confocal Microscopy List <[hidden email]> On Behalf Of Sylvie Le Guyader Sent: Tuesday, February 16, 2021 3:17 PM To: [hidden email] Subject: image manipulation ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Dear list I remember hearing or reading somewhere of a Fiji (maybe) plugin to help group leaders detect potential image manipulation but I cannot find what it was. Has anyone heard of it who could point me to the right direction? Med vänlig hälsning / Best regards Sylvie @@@@@@@@@@@@@@@@@@@@@@@@ Sylvie Le Guyader, PhD Live Cell Imaging Facility Manager Karolinska Institutet- Bionut Dpt Blickagången 16, Room 7362 (lab)/7840 (office) 14157 Huddinge, Sweden mobile: +46 (0) 73 733 5008 LCI website<https://ki.se/en/bionut/welcome-to-the-lci-facility> Follow our microscopy blog!<http://microscopykarolinska.se/> När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI's processing of personal data here<https://ki.se/en/staff/data-protection-policy>. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy |
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In reply to this post by Sylvie Le Guyader
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Hi Sylvie, I think that you might be referring to ORI Droplets that can be used in Fiji. https://ori.hhs.gov/droplets Cheers, Brian Armstrong PhD Associate Research Professor Developmental and Stem Cell Biology Diabetes and Metabolic Diseases Director, Light Microscopy Core Beckman Research Institute, City of Hope -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Sylvie Le Guyader Sent: Tuesday, February 16, 2021 6:17 AM To: [hidden email] Subject: image manipulation [Attention: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.] ---------------------------------------------------------------------- ***** To join, leave or search the confocal microscopy listserv, go to: https://urldefense.com/v3/__http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy__;!!Fou38LsQmgU!6uqFp_SB4aXrBYDXGifPrnhMgyX6WFoMfnfMQVa_Qnu0gYE9VQQGNiS3fRRVvCY$ Post images on https://urldefense.com/v3/__http://www.imgur.com__;!!Fou38LsQmgU!6uqFp_SB4aXrBYDXGifPrnhMgyX6WFoMfnfMQVa_Qnu0gYE9VQQGNiS3o1Gfc2w$ and include the link in your posting. ***** Dear list I remember hearing or reading somewhere of a Fiji (maybe) plugin to help group leaders detect potential image manipulation but I cannot find what it was. Has anyone heard of it who could point me to the right direction? Med vänlig hälsning / Best regards Sylvie @@@@@@@@@@@@@@@@@@@@@@@@ Sylvie Le Guyader, PhD Live Cell Imaging Facility Manager Karolinska Institutet- Bionut Dpt Blickagången 16, Room 7362 (lab)/7840 (office) 14157 Huddinge, Sweden mobile: +46 (0) 73 733 5008 LCI website<https://urldefense.com/v3/__https://ki.se/en/bionut/welcome-to-the-lci-facility__;!!Fou38LsQmgU!6uqFp_SB4aXrBYDXGifPrnhMgyX6WFoMfnfMQVa_Qnu0gYE9VQQGNiS3O2pmHog$ > Follow our microscopy blog!<https://urldefense.com/v3/__http://microscopykarolinska.se/__;!!Fou38LsQmgU!6uqFp_SB4aXrBYDXGifPrnhMgyX6WFoMfnfMQVa_Qnu0gYE9VQQGNiS38IZsI3I$ > När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://urldefense.com/v3/__https://ki.se/medarbetare/integritetsskyddspolicy__;!!Fou38LsQmgU!6uqFp_SB4aXrBYDXGifPrnhMgyX6WFoMfnfMQVa_Qnu0gYE9VQQGNiS3hKnKg-4$ >. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI's processing of personal data here<https://urldefense.com/v3/__https://ki.se/en/staff/data-protection-policy__;!!Fou38LsQmgU!6uqFp_SB4aXrBYDXGifPrnhMgyX6WFoMfnfMQVa_Qnu0gYE9VQQGNiS3PXfU9sM$ >. ---------------------------------------------------------------------- ------------------------------------------------------------ -SECURITY/CONFIDENTIALITY WARNING- This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (LCP301) ------------------------------------------------------------ |
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In reply to this post by Sylvie Le Guyader
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Hi Sylvie, - For a first quick check of images: https://29a.ch/photo-forensics/#forensic-magnifier - More detailed analysis * InspectJ in FIJI: https://github.com/ZMBH-Imaging-Facility/InspectJ * ORI Forensic tools: https://ori.hhs.gov/forensic-tools However, the ORI-tools are not recommended for teaching purposes as this is based on Photoshop actions and you want to keep any next generation life scientist away from Photoshop as long as possible as this is clearly NOT what should be used on scientific images. There are also commercial solutions. E.g Mike Rossner is now running a service…. Best regards, Oliver Oliver Biehlmaier, PhD | Head of Imaging Core Facility | Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel Phone: +41 61 207 20 73 | Email: [hidden email]<mailto:[hidden email]> | www.biozentrum.unibas.ch/imcf<http://www.biozentrum.unibas.ch/imcf> | www.microscopynetwork.unibas.ch<http://www.microscopynetwork.unibas.ch/> | https://www.ls2.ch/sections/microscopy | @imcf_basel<https://twitter.com/imcf_basel> | Online office: https://wiki.biozentrum.unibas.ch/x/YFYfCw | Email to [hidden email]<mailto:[hidden email]> to reach all IMCF-members On 16 Feb 2021, at 15:17, Sylvie Le Guyader <[hidden email]<mailto:[hidden email]>> wrote: ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Dear list I remember hearing or reading somewhere of a Fiji (maybe) plugin to help group leaders detect potential image manipulation but I cannot find what it was. Has anyone heard of it who could point me to the right direction? Med vänlig hälsning / Best regards Sylvie @@@@@@@@@@@@@@@@@@@@@@@@ Sylvie Le Guyader, PhD Live Cell Imaging Facility Manager Karolinska Institutet- Bionut Dpt Blickagången 16, Room 7362 (lab)/7840 (office) 14157 Huddinge, Sweden mobile: +46 (0) 73 733 5008 LCI website<https://ki.se/en/bionut/welcome-to-the-lci-facility> Follow our microscopy blog!<http://microscopykarolinska.se/> När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI's processing of personal data here<https://ki.se/en/staff/data-protection-policy>. |
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In reply to this post by Jeremy Adler-4
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Hi Jeremy and other listers, you don't really need any of these tricks to discern fraudulent images, as an extreme example see the figure 5d here [ https://www.sciencedirect.com/science/article/pii/S0920586118310848 ] or here if paywalled: [ https://scihubtw.tw/10.1016/j.cattod.2019.01.024 ] The curves are just scaled copies of the same curve, as pointed out here [ https://pubpeer.com/publications/71B5E2EF6A7716D7F7F3B273E86926 ], unbelievable! Worth noting, after couple retractions (e.g. Nature Communications, see [ https://pubmed.ncbi.nlm.nih.gov/33239646/ ]) and countless allegations of fraud, the group is still in business, publishing, receiving grants... Don't let anything like this happen (even unintentionally), as it could (and should) ruin your career! If anyone has a suspicion of undisclosed image manipulations in their group, just talk to your lab members. It's OK to make figures nicer and easier to understand, just don't hide it. Even photoshoping is fine, as long as you disclose it (well, the reviewers might not be happy, but you can respond in the rebuttal that "we achieved the same result in ImageJ by doing this, this and this..."). For honest and open science, zdenek On Tue, Feb 16, 2021 at 9:59 AM Jeremy Adler <[hidden email]> wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > Post images on http://www.imgur.com and include the link in your posting. > ***** > > Hej Sylvie, > > 1) look at the histogram for each channel > 2) use a variance filter - if bits have been cut and pasted from different > original images, the variance in the background may differ. > 3) a more sophisticated option is to look for the local poisson noise - > this should be the same in all areas of the image with a similar intensity > - but will differ if cutting and pasting has been used. > > However there is a competition between those committing fraud and those > chasing fraud - both improve. > There is also a major interest in comparing papers to check if the same > image has been re used. > > Jeremy > =============================================== > B i o V i s P l a t f o r m of Uppsala University > Light & EM microscopy / FlowCytometry & Cell Sorting / > Image Analysis > =============================================== > Jeremy Adler PhD - Senior research engineer > Light, Confocal Microscopy, Image Analysis > E-mail: [hidden email] > 070-1679349 > > Dag Hammarskjölds v 20 > 751 85 UPPSALA, SWEDEN > http://biovis.uu.se/ > =============================================== > > > > > > > > -----Original Message----- > From: Confocal Microscopy List <[hidden email]> On > Behalf Of Sylvie Le Guyader > Sent: Tuesday, February 16, 2021 3:17 PM > To: [hidden email] > Subject: image manipulation > > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > Post images on http://www.imgur.com and include the link in your posting. > ***** > > Dear list > > I remember hearing or reading somewhere of a Fiji (maybe) plugin to help > group leaders detect potential image manipulation but I cannot find what it > was. Has anyone heard of it who could point me to the right direction? > > Med vänlig hälsning / Best regards > > Sylvie > > @@@@@@@@@@@@@@@@@@@@@@@@ > Sylvie Le Guyader, PhD > Live Cell Imaging Facility Manager > Karolinska Institutet- Bionut Dpt > Blickagången 16, > Room 7362 (lab)/7840 (office) > 14157 Huddinge, Sweden > mobile: +46 (0) 73 733 5008 > LCI website<https://ki.se/en/bionut/welcome-to-the-lci-facility> > Follow our microscopy blog!<http://microscopykarolinska.se/> > > > > > När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI > kommer att behandla dina personuppgifter. Här finns information om hur KI > behandlar personuppgifter< > https://ki.se/medarbetare/integritetsskyddspolicy>. > > > Sending email to Karolinska Institutet (KI) will result in KI processing > your personal data. You can read more about KI's processing of personal > data here<https://ki.se/en/staff/data-protection-policy>. > > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så innebär > det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör > det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ > > E-mailing Uppsala University means that we will process your personal > data. For more information on how this is performed, please read here: > http://www.uu.se/en/about-uu/data-protection-policy > -- -- Zdenek Svindrych, Ph.D. Research Scientist - Microscopy Imaging Specialist Department of Biochemistry and Cell Biology Geisel School of Medicine at Dartmouth |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Dear Zdenek, I completely agree with your concluding statements in your post. Often, during image analysis, there are image processing steps that dramatically modify the image histogram and manipulate the images as part of the analysis workflow. However, I emphasis to the researchers I’m helping to document every step of the workflow and justify each step. This way, any image modification/manipulation is fully transparent and adequately justified for the reviewers and readers. In fact, I usually recommend to users to create an image stack that captures each modification made as a slice in that stack. The final stack can even be uploaded as supplementary images when possible. I believe that transparency is key. Cheers Yours sincerely, Praju Vikas Anekal. Ph.D. Biomed Imaging Microscopist/BioImage Analyst, Biomedical Imaging Research Unit. Faculty of Medical and Health Sciences, The University of Auckland. E-Mail : [hidden email]<mailto:[hidden email]> , Ext : 87831 From: Confocal Microscopy List <[hidden email]> On Behalf Of Zdenek Svindrych Sent: Wednesday, 17 February 2021 9:34 AM To: [hidden email] Subject: Re: image manipulation ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy<http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy> Post images on http://www.imgur.com<http://www.imgur.com> and include the link in your posting. ***** Hi Jeremy and other listers, you don't really need any of these tricks to discern fraudulent images, as an extreme example see the figure 5d here [ https://www.sciencedirect.com/science/article/pii/S0920586118310848<https://www.sciencedirect.com/science/article/pii/S0920586118310848> ] or here if paywalled: [ https://scihubtw.tw/10.1016/j.cattod.2019.01.024<https://scihubtw.tw/10.1016/j.cattod.2019.01.024> ] The curves are just scaled copies of the same curve, as pointed out here [ https://pubpeer.com/publications/71B5E2EF6A7716D7F7F3B273E86926<https://pubpeer.com/publications/71B5E2EF6A7716D7F7F3B273E86926> ], unbelievable! Worth noting, after couple retractions (e.g. Nature Communications, see [ https://pubmed.ncbi.nlm.nih.gov/33239646/<https://pubmed.ncbi.nlm.nih.gov/33239646> ]) and countless allegations of fraud, the group is still in business, publishing, receiving grants... Don't let anything like this happen (even unintentionally), as it could (and should) ruin your career! If anyone has a suspicion of undisclosed image manipulations in their group, just talk to your lab members. It's OK to make figures nicer and easier to understand, just don't hide it. Even photoshoping is fine, as long as you disclose it (well, the reviewers might not be happy, but you can respond in the rebuttal that "we achieved the same result in ImageJ by doing this, this and this..."). For honest and open science, zdenek On Tue, Feb 16, 2021 at 9:59 AM Jeremy Adler <[hidden email]<mailto:[hidden email]>> wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy<http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy> > Post images on http://www.imgur.com<http://www.imgur.com> and include the link in your posting. > ***** > > Hej Sylvie, > > 1) look at the histogram for each channel > 2) use a variance filter - if bits have been cut and pasted from different > original images, the variance in the background may differ. > 3) a more sophisticated option is to look for the local poisson noise - > this should be the same in all areas of the image with a similar intensity > - but will differ if cutting and pasting has been used. > > However there is a competition between those committing fraud and those > chasing fraud - both improve. > There is also a major interest in comparing papers to check if the same > image has been re used. > > Jeremy > =============================================== > B i o V i s P l a t f o r m of Uppsala University > Light & EM microscopy / FlowCytometry & Cell Sorting / > Image Analysis > =============================================== > Jeremy Adler PhD - Senior research engineer > Light, Confocal Microscopy, Image Analysis > E-mail: [hidden email]<mailto:[hidden email]> > 070-1679349 > > Dag Hammarskjölds v 20 > 751 85 UPPSALA, SWEDEN > http://biovis.uu.se/<http://biovis.uu.se> > =============================================== > > > > > > > > -----Original Message----- > From: Confocal Microscopy List <[hidden email]<mailto:[hidden email]>> On > Behalf Of Sylvie Le Guyader > Sent: Tuesday, February 16, 2021 3:17 PM > To: [hidden email]<mailto:[hidden email]> > Subject: image manipulation > > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy<http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy> > Post images on http://www.imgur.com<http://www.imgur.com> and include the link in your posting. > ***** > > Dear list > > I remember hearing or reading somewhere of a Fiji (maybe) plugin to help > group leaders detect potential image manipulation but I cannot find what it > was. Has anyone heard of it who could point me to the right direction? > > Med vänlig hälsning / Best regards > > Sylvie > > @@@@@@@@@@@@@@@@@@@@@@@@ > Sylvie Le Guyader, PhD > Live Cell Imaging Facility Manager > Karolinska Institutet- Bionut Dpt > Blickagången 16, > Room 7362 (lab)/7840 (office) > 14157 Huddinge, Sweden > mobile: +46 (0) 73 733 5008 > LCI website<https://ki.se/en/bionut/welcome-to-the-lci-facility<https://ki.se/en/bionut/welcome-to-the-lci-facility>> > Follow our microscopy blog!<http://microscopykarolinska.se/<http://microscopykarolinska.se>> > > > > > När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI > kommer att behandla dina personuppgifter. Här finns information om hur KI > behandlar personuppgifter< > https://ki.se/medarbetare/integritetsskyddspolicy<https://ki.se/medarbetare/integritetsskyddspolicy>>. > > > Sending email to Karolinska Institutet (KI) will result in KI processing > your personal data. You can read more about KI's processing of personal > data here<https://ki.se/en/staff/data-protection-policy<https://ki.se/en/staff/data-protection-policy>>. > > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så innebär > det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör > det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/<http://www.uu.se/om-uu/dataskydd-personuppgifter> > > E-mailing Uppsala University means that we will process your personal > data. For more information on how this is performed, please read here: > http://www.uu.se/en/about-uu/data-protection-policy<http://www.uu.se/en/about-uu/data-protection-policy> > -- -- Zdenek Svindrych, Ph.D. Research Scientist - Microscopy Imaging Specialist Department of Biochemistry and Cell Biology Geisel School of Medicine at Dartmouth |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** I really like Zdenek's supplemental movie stack idea. I've also used flow charts to show the processing steps along with a link for downloading a macro that does these steps: http://bit.ly/3jYyC4e Both of these ideas are a win-win, because not only does it clearly disclose your processing steps for people who may want to reproduce your analysis, but it also makes it much easier for the reviewers to understand how each step impacted the image. On Tue, Feb 16, 2021 at 2:10 PM Praju Vikas Anekal <[hidden email]> wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > Post images on http://www.imgur.com and include the link in your posting. > ***** > > Dear Zdenek, > > I completely agree with your concluding statements in your post. > > Often, during image analysis, there are image processing steps that > dramatically modify the image histogram and manipulate the images as part > of the analysis workflow. However, I emphasis to the researchers I’m > helping to document every step of the workflow and justify each step. This > way, any image modification/manipulation is fully transparent and > adequately justified for the reviewers and readers. > In fact, I usually recommend to users to create an image stack that > captures each modification made as a slice in that stack. The final stack > can even be uploaded as supplementary images when possible. > > I believe that transparency is key. > > Cheers > > Yours sincerely, > > Praju Vikas Anekal. Ph.D. > Biomed Imaging Microscopist/BioImage Analyst, Biomedical Imaging Research > Unit. > Faculty of Medical and Health Sciences, The University of Auckland. > E-Mail : [hidden email]<mailto:[hidden email]> , Ext : > 87831 > > From: Confocal Microscopy List <[hidden email]> On > Behalf Of Zdenek Svindrych > Sent: Wednesday, 17 February 2021 9:34 AM > To: [hidden email] > Subject: Re: image manipulation > > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy< > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy> > Post images on http://www.imgur.com<http://www.imgur.com> and include the > link in your posting. > ***** > > Hi Jeremy and other listers, > > you don't really need any of these tricks to discern fraudulent images, as > an extreme example see the figure 5d here > [ https://www.sciencedirect.com/science/article/pii/S0920586118310848< > https://www.sciencedirect.com/science/article/pii/S0920586118310848> ] > or here if paywalled: > [ https://scihubtw.tw/10.1016/j.cattod.2019.01.024< > https://scihubtw.tw/10.1016/j.cattod.2019.01.024> ] > The curves are just scaled copies of the same curve, as pointed out here [ > https://pubpeer.com/publications/71B5E2EF6A7716D7F7F3B273E86926< > https://pubpeer.com/publications/71B5E2EF6A7716D7F7F3B273E86926> ], > unbelievable! > > Worth noting, after couple retractions (e.g. Nature Communications, see [ > https://pubmed.ncbi.nlm.nih.gov/33239646/< > https://pubmed.ncbi.nlm.nih.gov/33239646> ]) and countless allegations of > fraud, the group is still in business, publishing, receiving grants... > > Don't let anything like this happen (even unintentionally), as it could > (and should) ruin your career! > > If anyone has a suspicion of undisclosed image manipulations in their > group, just talk to your lab members. It's OK to make figures nicer and > easier to understand, just don't hide it. Even photoshoping is fine, as > long as you disclose it (well, the reviewers might not be happy, but you > can respond in the rebuttal that "we achieved the same result in ImageJ by > doing this, this and this..."). > > For honest and open science, > zdenek > > > > On Tue, Feb 16, 2021 at 9:59 AM Jeremy Adler <[hidden email] > <mailto:[hidden email]>> wrote: > > > ***** > > To join, leave or search the confocal microscopy listserv, go to: > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy< > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy> > > Post images on http://www.imgur.com<http://www.imgur.com> and include > the link in your posting. > > ***** > > > > Hej Sylvie, > > > > 1) look at the histogram for each channel > > 2) use a variance filter - if bits have been cut and pasted from > different > > original images, the variance in the background may differ. > > 3) a more sophisticated option is to look for the local poisson noise - > > this should be the same in all areas of the image with a similar > intensity > > - but will differ if cutting and pasting has been used. > > > > However there is a competition between those committing fraud and those > > chasing fraud - both improve. > > There is also a major interest in comparing papers to check if the same > > image has been re used. > > > > Jeremy > > =============================================== > > B i o V i s P l a t f o r m of Uppsala University > > Light & EM microscopy / FlowCytometry & Cell Sorting / > > Image Analysis > > =============================================== > > Jeremy Adler PhD - Senior research engineer > > Light, Confocal Microscopy, Image Analysis > > E-mail: [hidden email]<mailto:[hidden email]> > > 070-1679349 > > > > Dag Hammarskjölds v 20 > > 751 85 UPPSALA, SWEDEN > > http://biovis.uu.se/<http://biovis.uu.se> > > =============================================== > > > > > > > > > > > > > > > > -----Original Message----- > > From: Confocal Microscopy List <[hidden email]<mailto: > [hidden email]>> On > > Behalf Of Sylvie Le Guyader > > Sent: Tuesday, February 16, 2021 3:17 PM > > To: [hidden email]<mailto: > [hidden email]> > > Subject: image manipulation > > > > ***** > > To join, leave or search the confocal microscopy listserv, go to: > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy< > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy> > > Post images on http://www.imgur.com<http://www.imgur.com> and include > the link in your posting. > > ***** > > > > Dear list > > > > I remember hearing or reading somewhere of a Fiji (maybe) plugin to help > > group leaders detect potential image manipulation but I cannot find what > it > > was. Has anyone heard of it who could point me to the right direction? > > > > Med vänlig hälsning / Best regards > > > > Sylvie > > > > @@@@@@@@@@@@@@@@@@@@@@@@ > > Sylvie Le Guyader, PhD > > Live Cell Imaging Facility Manager > > Karolinska Institutet- Bionut Dpt > > Blickagången 16, > > Room 7362 (lab)/7840 (office) > > 14157 Huddinge, Sweden > > mobile: +46 (0) 73 733 5008 > > LCI website<https://ki.se/en/bionut/welcome-to-the-lci-facility< > https://ki.se/en/bionut/welcome-to-the-lci-facility>> > > Follow our microscopy blog!<http://microscopykarolinska.se/< > http://microscopykarolinska.se>> > > > > > > > > > > När du skickar e-post till Karolinska Institutet (KI) innebär detta att > KI > > kommer att behandla dina personuppgifter. Här finns information om hur KI > > behandlar personuppgifter< > > https://ki.se/medarbetare/integritetsskyddspolicy< > https://ki.se/medarbetare/integritetsskyddspolicy>>. > > > > > > Sending email to Karolinska Institutet (KI) will result in KI processing > > your personal data. You can read more about KI's processing of personal > > data here<https://ki.se/en/staff/data-protection-policy< > https://ki.se/en/staff/data-protection-policy>>. > > > > > > > > > > > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så innebär > > det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör > > det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/< > http://www.uu.se/om-uu/dataskydd-personuppgifter> > > > > E-mailing Uppsala University means that we will process your personal > > data. For more information on how this is performed, please read here: > > http://www.uu.se/en/about-uu/data-protection-policy< > http://www.uu.se/en/about-uu/data-protection-policy> > > > > > -- > -- > Zdenek Svindrych, Ph.D. > Research Scientist - Microscopy Imaging Specialist > Department of Biochemistry and Cell Biology > Geisel School of Medicine at Dartmouth > -- Benjamin E. Smith, Ph. D. Imaging Specialist, Vision Science University of California, Berkeley 195 Weill Hall Berkeley, CA 94720-3200 Tel (510) 642-9712 Fax (510) 643-6791 e-mail: [hidden email] https://vision.berkeley.edu/faculty/core-grants-nei/core-grant-microscopic-imaging/ |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Hi Ben, yes, z-stack of image manipulation - great idea, not mine, though. Credits should go to Praju Vikas Anekal (Auckland? Does anybody know where that is? Austria?)... Sorry for the joke! zdenek On Tue, Feb 16, 2021 at 7:09 PM Benjamin Smith <[hidden email]> wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > Post images on http://www.imgur.com and include the link in your posting. > ***** > > I really like Zdenek's supplemental movie stack idea. I've also used flow > charts to show the processing steps along with a link for downloading a > macro that does these steps: http://bit.ly/3jYyC4e > > Both of these ideas are a win-win, because not only does it clearly > disclose your processing steps for people who may want to reproduce your > analysis, but it also makes it much easier for the reviewers to understand > how each step impacted the image. > > On Tue, Feb 16, 2021 at 2:10 PM Praju Vikas Anekal < > [hidden email]> > wrote: > > > ***** > > To join, leave or search the confocal microscopy listserv, go to: > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > > Post images on http://www.imgur.com and include the link in your > posting. > > ***** > > > > Dear Zdenek, > > > > I completely agree with your concluding statements in your post. > > > > Often, during image analysis, there are image processing steps that > > dramatically modify the image histogram and manipulate the images as part > > of the analysis workflow. However, I emphasis to the researchers I’m > > helping to document every step of the workflow and justify each step. > This > > way, any image modification/manipulation is fully transparent and > > adequately justified for the reviewers and readers. > > In fact, I usually recommend to users to create an image stack that > > captures each modification made as a slice in that stack. The final stack > > can even be uploaded as supplementary images when possible. > > > > I believe that transparency is key. > > > > Cheers > > > > Yours sincerely, > > > > Praju Vikas Anekal. Ph.D. > > Biomed Imaging Microscopist/BioImage Analyst, Biomedical Imaging Research > > Unit. > > Faculty of Medical and Health Sciences, The University of Auckland. > > E-Mail : [hidden email]<mailto:[hidden email]> , Ext : > > 87831 > > > > From: Confocal Microscopy List <[hidden email]> On > > Behalf Of Zdenek Svindrych > > Sent: Wednesday, 17 February 2021 9:34 AM > > To: [hidden email] > > Subject: Re: image manipulation > > > > ***** > > To join, leave or search the confocal microscopy listserv, go to: > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy< > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy> > > Post images on http://www.imgur.com<http://www.imgur.com> and include > the > > link in your posting. > > ***** > > > > Hi Jeremy and other listers, > > > > you don't really need any of these tricks to discern fraudulent images, > as > > an extreme example see the figure 5d here > > [ https://www.sciencedirect.com/science/article/pii/S0920586118310848< > > https://www.sciencedirect.com/science/article/pii/S0920586118310848> ] > > or here if paywalled: > > [ https://scihubtw.tw/10.1016/j.cattod.2019.01.024< > > https://scihubtw.tw/10.1016/j.cattod.2019.01.024> ] > > The curves are just scaled copies of the same curve, as pointed out here > [ > > https://pubpeer.com/publications/71B5E2EF6A7716D7F7F3B273E86926< > > https://pubpeer.com/publications/71B5E2EF6A7716D7F7F3B273E86926> ], > > unbelievable! > > > > Worth noting, after couple retractions (e.g. Nature Communications, see [ > > https://pubmed.ncbi.nlm.nih.gov/33239646/< > > https://pubmed.ncbi.nlm.nih.gov/33239646> ]) and countless allegations > of > > fraud, the group is still in business, publishing, receiving grants... > > > > Don't let anything like this happen (even unintentionally), as it could > > (and should) ruin your career! > > > > If anyone has a suspicion of undisclosed image manipulations in their > > group, just talk to your lab members. It's OK to make figures nicer and > > easier to understand, just don't hide it. Even photoshoping is fine, as > > long as you disclose it (well, the reviewers might not be happy, but you > > can respond in the rebuttal that "we achieved the same result in ImageJ > by > > doing this, this and this..."). > > > > For honest and open science, > > zdenek > > > > > > > > On Tue, Feb 16, 2021 at 9:59 AM Jeremy Adler <[hidden email] > > <mailto:[hidden email]>> wrote: > > > > > ***** > > > To join, leave or search the confocal microscopy listserv, go to: > > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy< > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy> > > > Post images on http://www.imgur.com<http://www.imgur.com> and include > > the link in your posting. > > > ***** > > > > > > Hej Sylvie, > > > > > > 1) look at the histogram for each channel > > > 2) use a variance filter - if bits have been cut and pasted from > > different > > > original images, the variance in the background may differ. > > > 3) a more sophisticated option is to look for the local poisson noise - > > > this should be the same in all areas of the image with a similar > > intensity > > > - but will differ if cutting and pasting has been used. > > > > > > However there is a competition between those committing fraud and those > > > chasing fraud - both improve. > > > There is also a major interest in comparing papers to check if the same > > > image has been re used. > > > > > > Jeremy > > > =============================================== > > > B i o V i s P l a t f o r m of Uppsala University > > > Light & EM microscopy / FlowCytometry & Cell Sorting / > > > Image Analysis > > > =============================================== > > > Jeremy Adler PhD - Senior research engineer > > > Light, Confocal Microscopy, Image Analysis > > > E-mail: [hidden email]<mailto:[hidden email]> > > > 070-1679349 > > > > > > Dag Hammarskjölds v 20 > > > 751 85 UPPSALA, SWEDEN > > > http://biovis.uu.se/<http://biovis.uu.se> > > > =============================================== > > > > > > > > > > > > > > > > > > > > > > > > -----Original Message----- > > > From: Confocal Microscopy List <[hidden email] > <mailto: > > [hidden email]>> On > > > Behalf Of Sylvie Le Guyader > > > Sent: Tuesday, February 16, 2021 3:17 PM > > > To: [hidden email]<mailto: > > [hidden email]> > > > Subject: image manipulation > > > > > > ***** > > > To join, leave or search the confocal microscopy listserv, go to: > > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy< > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy> > > > Post images on http://www.imgur.com<http://www.imgur.com> and include > > the link in your posting. > > > ***** > > > > > > Dear list > > > > > > I remember hearing or reading somewhere of a Fiji (maybe) plugin to > help > > > group leaders detect potential image manipulation but I cannot find > what > > it > > > was. Has anyone heard of it who could point me to the right direction? > > > > > > Med vänlig hälsning / Best regards > > > > > > Sylvie > > > > > > @@@@@@@@@@@@@@@@@@@@@@@@ > > > Sylvie Le Guyader, PhD > > > Live Cell Imaging Facility Manager > > > Karolinska Institutet- Bionut Dpt > > > Blickagången 16, > > > Room 7362 (lab)/7840 (office) > > > 14157 Huddinge, Sweden > > > mobile: +46 (0) 73 733 5008 > > > LCI website<https://ki.se/en/bionut/welcome-to-the-lci-facility< > > https://ki.se/en/bionut/welcome-to-the-lci-facility>> > > > Follow our microscopy blog!<http://microscopykarolinska.se/< > > http://microscopykarolinska.se>> > > > > > > > > > > > > > > > När du skickar e-post till Karolinska Institutet (KI) innebär detta att > > KI > > > kommer att behandla dina personuppgifter. Här finns information om hur > KI > > > behandlar personuppgifter< > > > https://ki.se/medarbetare/integritetsskyddspolicy< > > https://ki.se/medarbetare/integritetsskyddspolicy>>. > > > > > > > > > Sending email to Karolinska Institutet (KI) will result in KI > processing > > > your personal data. You can read more about KI's processing of personal > > > data here<https://ki.se/en/staff/data-protection-policy< > > https://ki.se/en/staff/data-protection-policy>>. > > > > > > > > > > > > > > > > > > > > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så innebär > > > det att vi behandlar dina personuppgifter. För att läsa mer om hur vi > gör > > > det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ > < > > http://www.uu.se/om-uu/dataskydd-personuppgifter> > > > > > > E-mailing Uppsala University means that we will process your personal > > > data. For more information on how this is performed, please read here: > > > http://www.uu.se/en/about-uu/data-protection-policy< > > http://www.uu.se/en/about-uu/data-protection-policy> > > > > > > > > > -- > > -- > > Zdenek Svindrych, Ph.D. > > Research Scientist - Microscopy Imaging Specialist > > Department of Biochemistry and Cell Biology > > Geisel School of Medicine at Dartmouth > > > > > -- > Benjamin E. Smith, Ph. D. > Imaging Specialist, Vision Science > University of California, Berkeley > 195 Weill Hall > Berkeley, CA 94720-3200 > Tel (510) 642-9712 > Fax (510) 643-6791 > e-mail: [hidden email] > > https://vision.berkeley.edu/faculty/core-grants-nei/core-grant-microscopic-imaging/ > -- -- Zdenek Svindrych, Ph.D. Research Scientist - Microscopy Imaging Specialist Department of Biochemistry and Cell Biology Geisel School of Medicine at Dartmouth |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Dear All, This "Z-stack of image manipulation" is indeed a great idea, however for this one would also need the appropriate tools. It is clear that you can't present such an "image processing stack" for all your data. If you think of a 3D multicolor, time-lapse movie, such an experimental file can be quite large and with a "processing stack" you would multiply the size of this file. The solution would be to select one representative (single plane, single color, single time point) image and demonstrate your process there. But: 1) Selecting a representative image is not easy, Not only conceptually but also technically. 2) The concept fails if you want to do a manipulation along the time axis.... Greetings Gabor -----Original Message----- From: Confocal Microscopy List <[hidden email]> On Behalf Of Zdenek Svindrych Sent: Wednesday, February 17, 2021 1:38 AM To: [hidden email] Subject: Re: image manipulation ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Hi Ben, yes, z-stack of image manipulation - great idea, not mine, though. Credits should go to Praju Vikas Anekal (Auckland? Does anybody know where that is? Austria?)... Sorry for the joke! zdenek On Tue, Feb 16, 2021 at 7:09 PM Benjamin Smith <[hidden email]> wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > Post images on http://www.imgur.com and include the link in your posting. > ***** > > I really like Zdenek's supplemental movie stack idea. I've also used > flow charts to show the processing steps along with a link for > downloading a macro that does these steps: http://bit.ly/3jYyC4e > > Both of these ideas are a win-win, because not only does it clearly > disclose your processing steps for people who may want to reproduce > your analysis, but it also makes it much easier for the reviewers to > understand how each step impacted the image. > > On Tue, Feb 16, 2021 at 2:10 PM Praju Vikas Anekal < > [hidden email]> > wrote: > > > ***** > > To join, leave or search the confocal microscopy listserv, go to: > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > > Post images on http://www.imgur.com and include the link in your > posting. > > ***** > > > > Dear Zdenek, > > > > I completely agree with your concluding statements in your post. > > > > Often, during image analysis, there are image processing steps that > > dramatically modify the image histogram and manipulate the images as > > part of the analysis workflow. However, I emphasis to the > > researchers I’m helping to document every step of the workflow and justify each step. > This > > way, any image modification/manipulation is fully transparent and > > adequately justified for the reviewers and readers. > > In fact, I usually recommend to users to create an image stack that > > captures each modification made as a slice in that stack. The final > > stack can even be uploaded as supplementary images when possible. > > > > I believe that transparency is key. > > > > Cheers > > > > Yours sincerely, > > > > Praju Vikas Anekal. Ph.D. > > Biomed Imaging Microscopist/BioImage Analyst, Biomedical Imaging > > Research Unit. > > Faculty of Medical and Health Sciences, The University of Auckland. > > E-Mail : [hidden email]<mailto:[hidden email]> , Ext : > > 87831 > > > > From: Confocal Microscopy List <[hidden email]> On > > Behalf Of Zdenek Svindrych > > Sent: Wednesday, 17 February 2021 9:34 AM > > To: [hidden email] > > Subject: Re: image manipulation > > > > ***** > > To join, leave or search the confocal microscopy listserv, go to: > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy< > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy> > > Post images on http://www.imgur.com<http://www.imgur.com> and > > include > the > > link in your posting. > > ***** > > > > Hi Jeremy and other listers, > > > > you don't really need any of these tricks to discern fraudulent > > images, > as > > an extreme example see the figure 5d here [ > > https://www.sciencedirect.com/science/article/pii/S0920586118310848< > > https://www.sciencedirect.com/science/article/pii/S0920586118310848> > > ] or here if paywalled: > > [ https://scihubtw.tw/10.1016/j.cattod.2019.01.024< > > https://scihubtw.tw/10.1016/j.cattod.2019.01.024> ] The curves are > > just scaled copies of the same curve, as pointed out here > [ > > https://pubpeer.com/publications/71B5E2EF6A7716D7F7F3B273E86926< > > https://pubpeer.com/publications/71B5E2EF6A7716D7F7F3B273E86926> ], > > unbelievable! > > > > Worth noting, after couple retractions (e.g. Nature Communications, > > see [ https://pubmed.ncbi.nlm.nih.gov/33239646/< > > https://pubmed.ncbi.nlm.nih.gov/33239646> ]) and countless > > allegations > of > > fraud, the group is still in business, publishing, receiving grants... > > > > Don't let anything like this happen (even unintentionally), as it > > could (and should) ruin your career! > > > > If anyone has a suspicion of undisclosed image manipulations in > > their group, just talk to your lab members. It's OK to make figures > > nicer and easier to understand, just don't hide it. Even > > photoshoping is fine, as long as you disclose it (well, the > > reviewers might not be happy, but you can respond in the rebuttal > > that "we achieved the same result in ImageJ > by > > doing this, this and this..."). > > > > For honest and open science, > > zdenek > > > > > > > > On Tue, Feb 16, 2021 at 9:59 AM Jeremy Adler <[hidden email] > > <mailto:[hidden email]>> wrote: > > > > > ***** > > > To join, leave or search the confocal microscopy listserv, go to: > > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy< > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy> > > > Post images on http://www.imgur.com<http://www.imgur.com> and > > > include > > the link in your posting. > > > ***** > > > > > > Hej Sylvie, > > > > > > 1) look at the histogram for each channel > > > 2) use a variance filter - if bits have been cut and pasted from > > different > > > original images, the variance in the background may differ. > > > 3) a more sophisticated option is to look for the local poisson > > > noise - this should be the same in all areas of the image with a > > > similar > > intensity > > > - but will differ if cutting and pasting has been used. > > > > > > However there is a competition between those committing fraud and > > > those chasing fraud - both improve. > > > There is also a major interest in comparing papers to check if the > > > same image has been re used. > > > > > > Jeremy > > > =============================================== > > > B i o V i s P l a t f o r m of Uppsala University Light & EM > > > microscopy / FlowCytometry & Cell Sorting / Image Analysis > > > =============================================== > > > Jeremy Adler PhD - Senior research engineer Light, Confocal > > > Microscopy, Image Analysis > > > E-mail: [hidden email]<mailto:[hidden email]> > > > 070-1679349 > > > > > > Dag Hammarskjölds v 20 > > > 751 85 UPPSALA, SWEDEN > > > http://biovis.uu.se/<http://biovis.uu.se> > > > =============================================== > > > > > > > > > > > > > > > > > > > > > > > > -----Original Message----- > > > From: Confocal Microscopy List <[hidden email] > <mailto: > > [hidden email]>> On > > > Behalf Of Sylvie Le Guyader > > > Sent: Tuesday, February 16, 2021 3:17 PM > > > To: [hidden email]<mailto: > > [hidden email]> > > > Subject: image manipulation > > > > > > ***** > > > To join, leave or search the confocal microscopy listserv, go to: > > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy< > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy> > > > Post images on http://www.imgur.com<http://www.imgur.com> and > > > include > > the link in your posting. > > > ***** > > > > > > Dear list > > > > > > I remember hearing or reading somewhere of a Fiji (maybe) plugin > > > to > help > > > group leaders detect potential image manipulation but I cannot > > > find > what > > it > > > was. Has anyone heard of it who could point me to the right direction? > > > > > > Med vänlig hälsning / Best regards > > > > > > Sylvie > > > > > > @@@@@@@@@@@@@@@@@@@@@@@@ > > > Sylvie Le Guyader, PhD > > > Live Cell Imaging Facility Manager Karolinska Institutet- Bionut > > > Dpt Blickagången 16, Room 7362 (lab)/7840 (office) > > > 14157 Huddinge, Sweden > > > mobile: +46 (0) 73 733 5008 > > > LCI website<https://ki.se/en/bionut/welcome-to-the-lci-facility< > > https://ki.se/en/bionut/welcome-to-the-lci-facility>> > > > Follow our microscopy blog!<http://microscopykarolinska.se/< > > http://microscopykarolinska.se>> > > > > > > > > > > > > > > > När du skickar e-post till Karolinska Institutet (KI) innebär > > > detta att > > KI > > > kommer att behandla dina personuppgifter. Här finns information om > > > hur > KI > > > behandlar personuppgifter< > > > https://ki.se/medarbetare/integritetsskyddspolicy< > > https://ki.se/medarbetare/integritetsskyddspolicy>>. > > > > > > > > > Sending email to Karolinska Institutet (KI) will result in KI > processing > > > your personal data. You can read more about KI's processing of > > > personal data here<https://ki.se/en/staff/data-protection-policy< > > https://ki.se/en/staff/data-protection-policy>>. > > > > > > > > > > > > > > > > > > > > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så > > > innebär det att vi behandlar dina personuppgifter. För att läsa > > > mer om hur vi > gör > > > det kan du läsa här: > > > http://www.uu.se/om-uu/dataskydd-personuppgifter/ > < > > http://www.uu.se/om-uu/dataskydd-personuppgifter> > > > > > > E-mailing Uppsala University means that we will process your > > > personal data. For more information on how this is performed, please read here: > > > http://www.uu.se/en/about-uu/data-protection-policy< > > http://www.uu.se/en/about-uu/data-protection-policy> > > > > > > > > > -- > > -- > > Zdenek Svindrych, Ph.D. > > Research Scientist - Microscopy Imaging Specialist Department of > > Biochemistry and Cell Biology Geisel School of Medicine at Dartmouth > > > > > -- > Benjamin E. Smith, Ph. D. > Imaging Specialist, Vision Science > University of California, Berkeley > 195 Weill Hall > Berkeley, CA 94720-3200 > Tel (510) 642-9712 > Fax (510) 643-6791 > e-mail: [hidden email] > > https://vision.berkeley.edu/faculty/core-grants-nei/core-grant-microsc > opic-imaging/ > -- -- Zdenek Svindrych, Ph.D. Research Scientist - Microscopy Imaging Specialist Department of Biochemistry and Cell Biology Geisel School of Medicine at Dartmouth |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Hi All, @Zdenek, That will be Auckland, New Zealand. ☺ Yes, we’ve had some troubles with being left off maps in the past. (As illustrated by this classic ad from NZ tourism a few years back) https://youtu.be/HynsTvRVLiI @Gabor, indeed once the dimensionality of the data goes beyond 3, such processing tracking becomes a whole lot harder. And as you suggested, the most feasible ‘workaround’ is to show these steps for one representative example. In my opinion, the most neutral way to select a ‘representative example’ is to determine the metric to be quantified from the images first. then only use an image that is no more than 1 stddev from the mean/median of said metric. This constrains your set of images you can use (hopefully ruling out outliers) but still allows you to choose a cell/image that clearly illustrates your hypothesis ( and may also be aesthetically pleasing as well). Yours sincerely, Praju Vikas Anekal. Ph.D. Biomed Imaging Microscopist/BioImage Analyst, Biomedical Imaging Research Unit. Faculty of Medical and Health Sciences, The University of Auckland. E-Mail : [hidden email]<mailto:[hidden email]> , Ext : 87831 From: Confocal Microscopy List <[hidden email]> On Behalf Of Csucs Gabor Sent: Wednesday, 17 February 2021 7:54 PM To: [hidden email] Subject: Re: image manipulation ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy<http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy> Post images on http://www.imgur.com<http://www.imgur.com> and include the link in your posting. ***** Dear All, This "Z-stack of image manipulation" is indeed a great idea, however for this one would also need the appropriate tools. It is clear that you can't present such an "image processing stack" for all your data. If you think of a 3D multicolor, time-lapse movie, such an experimental file can be quite large and with a "processing stack" you would multiply the size of this file. The solution would be to select one representative (single plane, single color, single time point) image and demonstrate your process there. But: 1) Selecting a representative image is not easy, Not only conceptually but also technically. 2) The concept fails if you want to do a manipulation along the time axis.... Greetings Gabor -----Original Message----- From: Confocal Microscopy List <[hidden email]<mailto:[hidden email]>> On Behalf Of Zdenek Svindrych Sent: Wednesday, February 17, 2021 1:38 AM To: [hidden email]<mailto:[hidden email]> Subject: Re: image manipulation ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy<http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy> Post images on http://www.imgur.com<http://www.imgur.com> and include the link in your posting. ***** Hi Ben, yes, z-stack of image manipulation - great idea, not mine, though. Credits should go to Praju Vikas Anekal (Auckland? Does anybody know where that is? Austria?)... Sorry for the joke! zdenek On Tue, Feb 16, 2021 at 7:09 PM Benjamin Smith <[hidden email]<mailto:[hidden email]>> wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy<http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy> > Post images on http://www.imgur.com<http://www.imgur.com> and include the link in your posting. > ***** > > I really like Zdenek's supplemental movie stack idea. I've also used > flow charts to show the processing steps along with a link for > downloading a macro that does these steps: http://bit.ly/3jYyC4e<http://bit.ly/3jYyC4e> > > Both of these ideas are a win-win, because not only does it clearly > disclose your processing steps for people who may want to reproduce > your analysis, but it also makes it much easier for the reviewers to > understand how each step impacted the image. > > On Tue, Feb 16, 2021 at 2:10 PM Praju Vikas Anekal < > [hidden email]<mailto:[hidden email]>> > wrote: > > > ***** > > To join, leave or search the confocal microscopy listserv, go to: > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy<http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy> > > Post images on http://www.imgur.com<http://www.imgur.com> and include the link in your > posting. > > ***** > > > > Dear Zdenek, > > > > I completely agree with your concluding statements in your post. > > > > Often, during image analysis, there are image processing steps that > > dramatically modify the image histogram and manipulate the images as > > part of the analysis workflow. However, I emphasis to the > > researchers I’m helping to document every step of the workflow and justify each step. > This > > way, any image modification/manipulation is fully transparent and > > adequately justified for the reviewers and readers. > > In fact, I usually recommend to users to create an image stack that > > captures each modification made as a slice in that stack. The final > > stack can even be uploaded as supplementary images when possible. > > > > I believe that transparency is key. > > > > Cheers > > > > Yours sincerely, > > > > Praju Vikas Anekal. Ph.D. > > Biomed Imaging Microscopist/BioImage Analyst, Biomedical Imaging > > Research Unit. > > Faculty of Medical and Health Sciences, The University of Auckland. > > E-Mail : [hidden email]<mailto:[hidden email]<mailto:[hidden email]%3cmailto:[hidden email]>> , Ext : > > 87831 > > > > From: Confocal Microscopy List <[hidden email]<mailto:[hidden email]>> On > > Behalf Of Zdenek Svindrych > > Sent: Wednesday, 17 February 2021 9:34 AM > > To: [hidden email]<mailto:[hidden email]> > > Subject: Re: image manipulation > > > > ***** > > To join, leave or search the confocal microscopy listserv, go to: > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy<http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>< > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy<http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>> > > Post images on http://www.imgur.com<http://www.imgur.com><http://www.imgur.com<http://www.imgur.com>> and > > include > the > > link in your posting. > > ***** > > > > Hi Jeremy and other listers, > > > > you don't really need any of these tricks to discern fraudulent > > images, > as > > an extreme example see the figure 5d here [ > > https://www.sciencedirect.com/science/article/pii/S0920586118310848<https://www.sciencedirect.com/science/article/pii/S0920586118310848>< > > https://www.sciencedirect.com/science/article/pii/S0920586118310848<https://www.sciencedirect.com/science/article/pii/S0920586118310848>> > > ] or here if paywalled: > > [ https://scihubtw.tw/10.1016/j.cattod.2019.01.024<https://scihubtw.tw/10.1016/j.cattod.2019.01.024>< > > https://scihubtw.tw/10.1016/j.cattod.2019.01.024<https://scihubtw.tw/10.1016/j.cattod.2019.01.024>> ] The curves are > > just scaled copies of the same curve, as pointed out here > [ > > https://pubpeer.com/publications/71B5E2EF6A7716D7F7F3B273E86926<https://pubpeer.com/publications/71B5E2EF6A7716D7F7F3B273E86926>< > > https://pubpeer.com/publications/71B5E2EF6A7716D7F7F3B273E86926<https://pubpeer.com/publications/71B5E2EF6A7716D7F7F3B273E86926>> ], > > unbelievable! > > > > Worth noting, after couple retractions (e.g. Nature Communications, > > see [ https://pubmed.ncbi.nlm.nih.gov/33239646/<https://pubmed.ncbi.nlm.nih.gov/33239646>< > > https://pubmed.ncbi.nlm.nih.gov/33239646<https://pubmed.ncbi.nlm.nih.gov/33239646>> ]) and countless > > allegations > of > > fraud, the group is still in business, publishing, receiving grants... > > > > Don't let anything like this happen (even unintentionally), as it > > could (and should) ruin your career! > > > > If anyone has a suspicion of undisclosed image manipulations in > > their group, just talk to your lab members. It's OK to make figures > > nicer and easier to understand, just don't hide it. Even > > photoshoping is fine, as long as you disclose it (well, the > > reviewers might not be happy, but you can respond in the rebuttal > > that "we achieved the same result in ImageJ > by > > doing this, this and this..."). > > > > For honest and open science, > > zdenek > > > > > > > > On Tue, Feb 16, 2021 at 9:59 AM Jeremy Adler <[hidden email] > > > > > ***** > > > To join, leave or search the confocal microscopy listserv, go to: > > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy<http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>< > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy<http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>> > > > Post images on http://www.imgur.com<http://www.imgur.com><http://www.imgur.com<http://www.imgur.com>> and > > > include > > the link in your posting. > > > ***** > > > > > > Hej Sylvie, > > > > > > 1) look at the histogram for each channel > > > 2) use a variance filter - if bits have been cut and pasted from > > different > > > original images, the variance in the background may differ. > > > 3) a more sophisticated option is to look for the local poisson > > > noise - this should be the same in all areas of the image with a > > > similar > > intensity > > > - but will differ if cutting and pasting has been used. > > > > > > However there is a competition between those committing fraud and > > > those chasing fraud - both improve. > > > There is also a major interest in comparing papers to check if the > > > same image has been re used. > > > > > > Jeremy > > > =============================================== > > > B i o V i s P l a t f o r m of Uppsala University Light & EM > > > microscopy / FlowCytometry & Cell Sorting / Image Analysis > > > =============================================== > > > Jeremy Adler PhD - Senior research engineer Light, Confocal > > > Microscopy, Image Analysis > > > E-mail: [hidden email]<mailto:[hidden email]<mailto:[hidden email]%3cmailto:[hidden email]>> > > > 070-1679349 > > > > > > Dag Hammarskjölds v 20 > > > 751 85 UPPSALA, SWEDEN > > > http://biovis.uu.se/<http://biovis.uu.se><http://biovis.uu.se<http://biovis.uu.se>> > > > =============================================== > > > > > > > > > > > > > > > > > > > > > > > > -----Original Message----- > > > From: Confocal Microscopy List <[hidden email] <mailto:%0b>> > [hidden email]<mailto:[hidden email]>>> On > > > Behalf Of Sylvie Le Guyader > > > Sent: Tuesday, February 16, 2021 3:17 PM > > > To: [hidden email]<mailto<mailto:[hidden email]%3cmailto>: > > [hidden email]<mailto:[hidden email]>> > > > Subject: image manipulation > > > > > > ***** > > > To join, leave or search the confocal microscopy listserv, go to: > > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy<http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>< > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy<http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>> > > > Post images on http://www.imgur.com<http://www.imgur.com><http://www.imgur.com<http://www.imgur.com>> and > > > include > > the link in your posting. > > > ***** > > > > > > Dear list > > > > > > I remember hearing or reading somewhere of a Fiji (maybe) plugin > > > to > help > > > group leaders detect potential image manipulation but I cannot > > > find > what > > it > > > was. Has anyone heard of it who could point me to the right direction? > > > > > > Med vänlig hälsning / Best regards > > > > > > Sylvie > > > > > > @@@@@@@@@@@@@@@@@@@@@@@@ > > > Sylvie Le Guyader, PhD > > > Live Cell Imaging Facility Manager Karolinska Institutet- Bionut > > > Dpt Blickagången 16, Room 7362 (lab)/7840 (office) > > > 14157 Huddinge, Sweden > > > mobile: +46 (0) 73 733 5008 > > > LCI website<https://ki.se/en/bionut/welcome-to-the-lci-facility<https://ki.se/en/bionut/welcome-to-the-lci-facility>< > > https://ki.se/en/bionut/welcome-to-the-lci-facility<https://ki.se/en/bionut/welcome-to-the-lci-facility>>> > > > Follow our microscopy blog!<http://microscopykarolinska.se/<http://microscopykarolinska.se>< > > http://microscopykarolinska.se<http://microscopykarolinska.se>>> > > > > > > > > > > > > > > > När du skickar e-post till Karolinska Institutet (KI) innebär > > > detta att > > KI > > > kommer att behandla dina personuppgifter. Här finns information om > > > hur > KI > > > behandlar personuppgifter< > > > https://ki.se/medarbetare/integritetsskyddspolicy<https://ki.se/medarbetare/integritetsskyddspolicy>< > > https://ki.se/medarbetare/integritetsskyddspolicy<https://ki.se/medarbetare/integritetsskyddspolicy>>>. > > > > > > > > > Sending email to Karolinska Institutet (KI) will result in KI > processing > > > your personal data. You can read more about KI's processing of > > > personal data here<https://ki.se/en/staff/data-protection-policy<https://ki.se/en/staff/data-protection-policy>< > > https://ki.se/en/staff/data-protection-policy<https://ki.se/en/staff/data-protection-policy>>>. > > > > > > > > > > > > > > > > > > > > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så > > > innebär det att vi behandlar dina personuppgifter. För att läsa > > > mer om hur vi > gör > > > det kan du läsa här: > > > http://www.uu.se/om-uu/dataskydd-personuppgifter/<http://www.uu.se/om-uu/dataskydd-personuppgifter> > < > > http://www.uu.se/om-uu/dataskydd-personuppgifter<http://www.uu.se/om-uu/dataskydd-personuppgifter>> > > > > > > E-mailing Uppsala University means that we will process your > > > personal data. For more information on how this is performed, please read here: > > > http://www.uu.se/en/about-uu/data-protection-policy<http://www.uu.se/en/about-uu/data-protection-policy>< > > http://www.uu.se/en/about-uu/data-protection-policy<http://www.uu.se/en/about-uu/data-protection-policy>> > > > > > > > > > -- > > -- > > Zdenek Svindrych, Ph.D. > > Research Scientist - Microscopy Imaging Specialist Department of > > Biochemistry and Cell Biology Geisel School of Medicine at Dartmouth > > > > > -- > Benjamin E. Smith, Ph. D. > Imaging Specialist, Vision Science > University of California, Berkeley > 195 Weill Hall > Berkeley, CA 94720-3200 > Tel (510) 642-9712 > Fax (510) 643-6791 > e-mail: [hidden email]<mailto:[hidden email]> > > https://vision.berkeley.edu/faculty/core-grants-nei/core-grant-microsc<https://vision.berkeley.edu/faculty/core-grants-nei/core-grant-microsc> > opic-imaging/ > -- -- Zdenek Svindrych, Ph.D. Research Scientist - Microscopy Imaging Specialist Department of Biochemistry and Cell Biology Geisel School of Medicine at Dartmouth |
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In reply to this post by Benjamin Smith
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Hi All I think the best approach is to keep primary data together with the program script that produces the final image in the same folder. We use to use IDL but have switched to Matlab for all image processing and analysis so our code is available and code parts can be re-used easily (such as complicated segmentation routines). Of course there is a steep learning curve to using/developing such scripts but at least we can be sure of the reproducibility of the results and no intermediate images need to be stored so it's very space efficient. The downsides might be: 1) Steep learning curves (but the increased depth of understanding offsets this). Most undergrads I've met are able to get to grips with simple image processing in these environments. 2) Time -to write a program to open a data set, gaussian filter it and store the results take a bit longer than clicking on buttons in imagej. This difference disappears if many images need to be processed in the same way. 3) Cost -some universities have site licenses but if you have to pay for the license it is a problem if it's not been budgeted for in grants. I know that Python/scipy is free tool that is powerful but the learning curve is (I think) steeper because it's somewhat lower level than IDL/Matlab plus generally weak documentation and poor user interface. There may be fewer user submitted and tested library routines but it may improve in this regard. I'm not sure how easy it is to develop complicated image processing programs in this environment (you get what you pay for) and since I've never encountered anything that can't be done with matlab plus extensions I've never felt the need to get to grips with python/scipy/numpy even as it evolves. 4) Reluctance to get to grips with programming -but the computer is the slide rule of today's scientist so why not learn to unleash its full power if you want to be a professional scientist? 5) Lack of local support in use of the tool -but help groups exist although don't expect much help if you don't try to RTFM. I have no commercial interest in any of the solutions mentioned. My 2c Cheers Mark Mark B. Cannell. Ph.D. FRSNZ FISHR Department of Physiology, Pharmacology & Neuroscience School of Medical Sciences University Walk Bristol BS8 1TD [hidden email] On 17/02/21, 12:09 AM, "Confocal Microscopy List on behalf of Benjamin Smith" <[hidden email] on behalf of [hidden email]> wrote: ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** I really like Zdenek's supplemental movie stack idea. I've also used flow charts to show the processing steps along with a link for downloading a macro that does these steps: http://bit.ly/3jYyC4e Both of these ideas are a win-win, because not only does it clearly disclose your processing steps for people who may want to reproduce your analysis, but it also makes it much easier for the reviewers to understand how each step impacted the image. On Tue, Feb 16, 2021 at 2:10 PM Praju Vikas Anekal <[hidden email]> wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > Post images on http://www.imgur.com and include the link in your posting. > ***** > > Dear Zdenek, > > I completely agree with your concluding statements in your post. > > Often, during image analysis, there are image processing steps that > dramatically modify the image histogram and manipulate the images as part > of the analysis workflow. However, I emphasis to the researchers I’m > helping to document every step of the workflow and justify each step. This > way, any image modification/manipulation is fully transparent and > adequately justified for the reviewers and readers. > In fact, I usually recommend to users to create an image stack that > captures each modification made as a slice in that stack. The final stack > can even be uploaded as supplementary images when possible. > > I believe that transparency is key. > > Cheers > > Yours sincerely, > > Praju Vikas Anekal. Ph.D. > Biomed Imaging Microscopist/BioImage Analyst, Biomedical Imaging Research > Unit. > Faculty of Medical and Health Sciences, The University of Auckland. > E-Mail : [hidden email]<mailto:[hidden email]> , Ext : > 87831 > > From: Confocal Microscopy List <[hidden email]> On > Behalf Of Zdenek Svindrych > Sent: Wednesday, 17 February 2021 9:34 AM > To: [hidden email] > Subject: Re: image manipulation > > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy< > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy> > Post images on http://www.imgur.com<http://www.imgur.com> and include the > link in your posting. > ***** > > Hi Jeremy and other listers, > > you don't really need any of these tricks to discern fraudulent images, as > an extreme example see the figure 5d here > [ https://www.sciencedirect.com/science/article/pii/S0920586118310848< > https://www.sciencedirect.com/science/article/pii/S0920586118310848> ] > or here if paywalled: > [ https://scihubtw.tw/10.1016/j.cattod.2019.01.024< > https://scihubtw.tw/10.1016/j.cattod.2019.01.024> ] > The curves are just scaled copies of the same curve, as pointed out here [ > https://pubpeer.com/publications/71B5E2EF6A7716D7F7F3B273E86926< > https://pubpeer.com/publications/71B5E2EF6A7716D7F7F3B273E86926> ], > unbelievable! > > Worth noting, after couple retractions (e.g. Nature Communications, see [ > https://pubmed.ncbi.nlm.nih.gov/33239646/< > https://pubmed.ncbi.nlm.nih.gov/33239646> ]) and countless allegations of > fraud, the group is still in business, publishing, receiving grants... > > Don't let anything like this happen (even unintentionally), as it could > (and should) ruin your career! > > If anyone has a suspicion of undisclosed image manipulations in their > group, just talk to your lab members. It's OK to make figures nicer and > easier to understand, just don't hide it. Even photoshoping is fine, as > long as you disclose it (well, the reviewers might not be happy, but you > can respond in the rebuttal that "we achieved the same result in ImageJ by > doing this, this and this..."). > > For honest and open science, > zdenek > > > > On Tue, Feb 16, 2021 at 9:59 AM Jeremy Adler <[hidden email] > <mailto:[hidden email]>> wrote: > > > ***** > > To join, leave or search the confocal microscopy listserv, go to: > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy< > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy> > > Post images on http://www.imgur.com<http://www.imgur.com> and include > the link in your posting. > > ***** > > > > Hej Sylvie, > > > > 1) look at the histogram for each channel > > 2) use a variance filter - if bits have been cut and pasted from > different > > original images, the variance in the background may differ. > > 3) a more sophisticated option is to look for the local poisson noise - > > this should be the same in all areas of the image with a similar > intensity > > - but will differ if cutting and pasting has been used. > > > > However there is a competition between those committing fraud and those > > chasing fraud - both improve. > > There is also a major interest in comparing papers to check if the same > > image has been re used. > > > > Jeremy > > =============================================== > > B i o V i s P l a t f o r m of Uppsala University > > Light & EM microscopy / FlowCytometry & Cell Sorting / > > Image Analysis > > =============================================== > > Jeremy Adler PhD - Senior research engineer > > Light, Confocal Microscopy, Image Analysis > > E-mail: [hidden email]<mailto:[hidden email]> > > 070-1679349 > > > > Dag Hammarskjölds v 20 > > 751 85 UPPSALA, SWEDEN > > http://biovis.uu.se/<http://biovis.uu.se> > > =============================================== > > > > > > > > > > > > > > > > -----Original Message----- > > From: Confocal Microscopy List <[hidden email]<mailto: > [hidden email]>> On > > Behalf Of Sylvie Le Guyader > > Sent: Tuesday, February 16, 2021 3:17 PM > > To: [hidden email]<mailto: > [hidden email]> > > Subject: image manipulation > > > > ***** > > To join, leave or search the confocal microscopy listserv, go to: > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy< > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy> > > Post images on http://www.imgur.com<http://www.imgur.com> and include > the link in your posting. > > ***** > > > > Dear list > > > > I remember hearing or reading somewhere of a Fiji (maybe) plugin to help > > group leaders detect potential image manipulation but I cannot find what > it > > was. Has anyone heard of it who could point me to the right direction? > > > > Med vänlig hälsning / Best regards > > > > Sylvie > > > > @@@@@@@@@@@@@@@@@@@@@@@@ > > Sylvie Le Guyader, PhD > > Live Cell Imaging Facility Manager > > Karolinska Institutet- Bionut Dpt > > Blickagången 16, > > Room 7362 (lab)/7840 (office) > > 14157 Huddinge, Sweden > > mobile: +46 (0) 73 733 5008 > > LCI website<https://ki.se/en/bionut/welcome-to-the-lci-facility< > https://ki.se/en/bionut/welcome-to-the-lci-facility>> > > Follow our microscopy blog!<http://microscopykarolinska.se/< > http://microscopykarolinska.se>> > > > > > > > > > > När du skickar e-post till Karolinska Institutet (KI) innebär detta att > KI > > kommer att behandla dina personuppgifter. Här finns information om hur KI > > behandlar personuppgifter< > > https://ki.se/medarbetare/integritetsskyddspolicy< > https://ki.se/medarbetare/integritetsskyddspolicy>>. > > > > > > Sending email to Karolinska Institutet (KI) will result in KI processing > > your personal data. You can read more about KI's processing of personal > > data here<https://ki.se/en/staff/data-protection-policy< > https://ki.se/en/staff/data-protection-policy>>. > > > > > > > > > > > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så innebär > > det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör > > det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/< > http://www.uu.se/om-uu/dataskydd-personuppgifter> > > > > E-mailing Uppsala University means that we will process your personal > > data. For more information on how this is performed, please read here: > > http://www.uu.se/en/about-uu/data-protection-policy< > http://www.uu.se/en/about-uu/data-protection-policy> > > > > > -- > -- > Zdenek Svindrych, Ph.D. > Research Scientist - Microscopy Imaging Specialist > Department of Biochemistry and Cell Biology > Geisel School of Medicine at Dartmouth > -- Benjamin E. Smith, Ph. D. Imaging Specialist, Vision Science University of California, Berkeley 195 Weill Hall Berkeley, CA 94720-3200 Tel (510) 642-9712 Fax (510) 643-6791 e-mail: [hidden email] https://vision.berkeley.edu/faculty/core-grants-nei/core-grant-microscopic-imaging/ |
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