*****
To join or leave the confocal microscopy listserv or to change your email address, go to:
https://lists.umn.edu/cgi-bin/wa?SUBED1=confocalmicroscopy&A=1
Post images on http://www.imgur.com and include the link in your posting.
*****
Hi Brian and Lutz,
Just now catching-up on the recent messages. I believe that Thomas addressed some of the earlier points. Let me explain a bit more about the study design. Most quantitative image analysis of microscopy images is currently performed by the people who acquired the images, most of whom are not image analysis experts. The study was therefore modeled from the point-of-view of someone who took some images and then wanted to segment them. We wanted to assess the variability in segmentation results in this "real-life" situation--not with a panel of image analysis experts alone, but with participants with a diverse range of experience levels. (Now, whether image analysis should actually be done by non-experts is open to debate, but beside the point of the study since this is not what currently occurs.) Essentially, we're asking, "If we give the same images to a bunch of people, will they all produce the same segmentation?" Obviously the answer is, "no" - they will be different - but how different?
Lutz - we're not as concerned with "best" results as much as the consistency between results (accuracy vs. precision). We're not trying to identify any one algorithm that works better than the others (although one could assess accuracy relative to the ground truth). As you mention, it will be extremely difficult (nigh impossible) to attribute variability conclusively to a specific component or set of components. The study was not designed to make firm conclusions about causation. Nevertheless, we are hopeful that our analyses will yield clues that can then be tested in follow-up studies/experiments by us and the image analysis community. I should point-out that we are collecting a large amount of survey data in addition to the actual segmentation results. These data will be interesting in their own right as they might speak to, e.g., an analyst's under-/over-confidence in segmentation accuracy and common themes in segmentation pipelines. They will also be useful when comparing to the segmentation results - e.g. if variability correlates with image analysis experience etc.
This study was always intended to be a first step - just trying to get a handle on the magnitude of the problem - and not the conclusive work on the sources and solutions of variability in image analysis.
-Kris
________________________________
From: [log in to unmask] <[log in to unmask]>
Sent: Saturday, April 23, 2022 6:01 PM
Subject: Re: 3D Image Analysis Tools and Reproducibility Event - April 27th via Zoom
*****
To join or leave the confocal microscopy listserv or to change your email address, go to:
https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.umn.edu_cgi-2Dbin_wa-3FSUBED1-3Dconfocalmicroscopy-26A-3D1&d=DwIFaQ&c=eLbWYnpnzycBCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJsl0IvoA&m=ujLhFVlRizFeEkHaIJ0lk-QEBm9LowvE-ljMIr1V-o8&s=Hble3y1wAIBN3iELJ0GtjYGmU61ISQoEdVk9N9tHYnY&e=
Post images on https://urldefense.proofpoint.com/v2/url?u=http-3A__www.imgur.com&d=DwIFaQ&c=eLbWYnpnzycBCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJsl0IvoA&m=ujLhFVlRizFeEkHaIJ0lk-QEBm9LowvE-ljMIr1V-o8&s=8eoPW-urqaPARZRE8fkq26gERjoK0kxkhPa7tl_H0HA&e= and include the link in your posting.
*****
Brian,
Understood, the objective is "best results" with human factor plus instrumentation variability. Sounds interesting in a way to get an idea about image quality distribution among the labs under study. It seems though that the result this study seeks is fundamentally underdetermined and therefore a conclusion could be biased to say the least. As you mention segmentation trying next to deconvolution to solve ill-posed problems thrown in this looks very messy to me. Also what is the metric for measuring "best results"? Are the participants given simulations with known ground truths, so the best fit could indeed be determined? Just saying this because there had been challenges tendered online to improve algorithms using complex simulations.
>> I am curious, if the study shows high variability in results, then what
>> will the organizers do with the information? Will you make
>> recommendations as to how to improve the situation? What will the solution be?"
As I said, there are just too many variables to predict how the spread will be distributed. I wouldn’t even expect a natural (i.e. Gaussian or Poisson like) distribution because there are no linear dependencies. I am not a statistician but I think not even by statistical laws this problem is mathematically tractable to draw any conclusion, let alone recommendations. The only one I could come up with is to set highest standards in image understanding, from sample preparation to result interpretation. This can only be achieved in specialized interdisciplinary teams of experts.
Sorry, that’s about all I could say to this undertaking...
Regards
Lutz
-----Original Message-----
From: Confocal Microscopy List <[log in to unmask]> On Behalf Of Brian Northan
Sent: Saturday, April 23, 2022 5:00 PM
To: [log in to unmask]
Subject: Re: 3D Image Analysis Tools and Reproducibility Event - April 27th via Zoom
*****
To join or leave the confocal microscopy listserv or to change your email address, go to:
https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.umn.edu_cgi-2Dbin_wa-3FSUBED1-3Dconfocalmicroscopy-26A-3D1&d=DwIFaQ&c=eLbWYnpnzycBCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJsl0IvoA&m=ujLhFVlRizFeEkHaIJ0lk-QEBm9LowvE-ljMIr1V-o8&s=Hble3y1wAIBN3iELJ0GtjYGmU61ISQoEdVk9N9tHYnY&e=
Post images on https://urldefense.proofpoint.com/v2/url?u=http-3A__www.imgur.com&d=DwIFaQ&c=eLbWYnpnzycBCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJsl0IvoA&m=ujLhFVlRizFeEkHaIJ0lk-QEBm9LowvE-ljMIr1V-o8&s=8eoPW-urqaPARZRE8fkq26gERjoK0kxkhPa7tl_H0HA&e= and include the link in your posting.
*****
Hi Lutz
The organizers of the study did not intend users to test PSF generation or deconvolution, or any specific algorithms, my understanding is they just want to measure how much variability there is in results. Given the same
image, how different are the results that people generate? I don't think
participants were given any specific direction as to what algorithm or workflow to use, they had to choose themselves, which I guess is one of the sources of variability the study is trying to measure.
I brought attention to deconvolution and PSF generation, because I could not deconvolve the images using Richardson Lucy deconvolution and a
theoretical PSF. Independent of the study, I saw discussions as to the
best way to segment the study images, for example one person suggested a deep learning tool called StarDist, another background subtraction followed by watershed, neither of those approaches restored intensities and only provided rough estimates of the structure, I thought it would make sense to try Richardson Lucy Deconvolution before segmenting. However this was complicated by the issue with the PSF used in the simulation.
Even though the purpose of the study was to measure user variability, not algorithm performance, when given these test images, people will naturally experiment and try to find the best method, so it's important the meta data
be correct to facilitate fair comparison. Thus my reason for being
involved in the conversation.
I am curious, if the study shows high variability in results, then what
will the organizers do with the information? Will you make
recommendations as to how to improve the situation? What will the solution be?
Brian
On Sat, Apr 23, 2022 at 8:47 AM <[log in to unmask]> wrote:
> *****
> To join or leave the confocal microscopy listserv or to change your
> email address, go to:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.umn.edu_cgi-2Dbin_wa-3FSUBED1-3Dconfocalmicroscopy-26A-3D1&d=DwIFaQ&c=eLbWYnpnzycBCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJsl0IvoA&m=ujLhFVlRizFeEkHaIJ0lk-QEBm9LowvE-ljMIr1V-o8&s=Hble3y1wAIBN3iELJ0GtjYGmU61ISQoEdVk9N9tHYnY&e=
> Post images on https://urldefense.proofpoint.com/v2/url?u=http-3A__www.imgur.com&d=DwIFaQ&c=eLbWYnpnzycBCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJsl0IvoA&m=ujLhFVlRizFeEkHaIJ0lk-QEBm9LowvE-ljMIr1V-o8&s=8eoPW-urqaPARZRE8fkq26gERjoK0kxkhPa7tl_H0HA&e= and include the link in your posting.
> *****
>
> Following this thread for a while, I feel compelled to question how a
> random study of the performance of various PSF generation- and
> deconvolution algorithms would be helpful? Randomized studies are
> relevant in life science to find statistical distributions of
> otherwise indeterminate behavior. Except for machine learning,
> algorithms are developed to reconstruct sample representations based
> on strictly deterministic mathematical models. If I understand
> correctly, this "reproducibility determination study" is based on how
> a number of available software implementations perform without
> considering the developmental background among them, notwithstanding
> even if they are buggy or contain systemic faults. I do understand
> however that there is a need for scientists using tools from other
> scientific areas and communities in knowing which implementations
> perform best. In that case, the random part should not be the
> implementations of algorithms because they are within themselves at least somewhat deterministic...
>
> Regards
> Lutz
>
> -----Original Message-----
> From: Confocal Microscopy List <[log in to unmask]> On
> Behalf Of Thomas Pengo
> Sent: Friday, April 22, 2022 9:45 PM
> To: [log in to unmask]
> Subject: Re: 3D Image Analysis Tools and Reproducibility Event - April
> 27th via Zoom
>
> *****
> To join or leave the confocal microscopy listserv or to change your
> email address, go to:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.umn.edu_cgi-2Dbin_wa-3FSUBED1-3Dconfocalmicroscopy-26A-3D1&d=DwIFaQ&c=eLbWYnpnzycBCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJsl0IvoA&m=ujLhFVlRizFeEkHaIJ0lk-QEBm9LowvE-ljMIr1V-o8&s=Hble3y1wAIBN3iELJ0GtjYGmU61ISQoEdVk9N9tHYnY&e=
> Post images on https://urldefense.proofpoint.com/v2/url?u=http-3A__www.imgur.com&d=DwIFaQ&c=eLbWYnpnzycBCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJsl0IvoA&m=ujLhFVlRizFeEkHaIJ0lk-QEBm9LowvE-ljMIr1V-o8&s=8eoPW-urqaPARZRE8fkq26gERjoK0kxkhPa7tl_H0HA&e= and include the link in your posting.
> *****
>
> Hi Brian
>
> Thanks for your comments so far and your work on the study’s images.
>
> I have been helping with the generation of the study’s images and
> wanted to add some background. We chose not to reinvent the wheel and
> use an existing open source software, Cytopacq, which has also been
> used before in other studies. Rather than use the online generator, we
> preferred to use the command line version that would allow us to
> record a configuration file and use a custom PSF file. We generated a
> PSF using another open source software, PSF Generator. After you
> raised your concerns, we started to look into it but didn’t get very
> far at the time. My availability was limited and I have only recently
> been able to get back to the issue. At the time, we deemed it was not
> invalidating the study as the point of it was, unlike a traditional
> challenge, to investigate how different researchers would get
> different results given the same task. I agree reproducibility in the
> narrow sense implies that were looking for a perfect ability to replay
> a given approach step by step, but I do believe this variability study
> does fall under the same broader problem of reporting results
> completely and correctly, applicability of a given method to a
> different domain, generalizability, …
>
> To your point, we’re trying another approach that hopefully will serve
> your purpose. We are trying to generate an “experimental PSF”, by
> using a microsphere phantom. One one hand it would allow you and
> others to perform hopefully a more successful deconvolution, and on
> the other to study the mismatch between expected and actual results.
>
> I hope to have some more to report early next week.
>
> Thomas
>
>
>
>
> On Fri, Apr 22, 2022 at 2:56 PM Brian Northan <[log in to unmask]> wrote:
>
> > *****
> > To join or leave the confocal microscopy listserv or to change your
> > email address, go to:
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.umn.edu_cgi-2Dbin_wa-3FSUBED1-3Dconfocalmicroscopy-26A-3D1&d=DwIFaQ&c=eLbWYnpnzycBCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJsl0IvoA&m=ujLhFVlRizFeEkHaIJ0lk-QEBm9LowvE-ljMIr1V-o8&s=Hble3y1wAIBN3iELJ0GtjYGmU61ISQoEdVk9N9tHYnY&e=
> > Post images on https://urldefense.proofpoint.com/v2/url?u=http-3A__www.imgur.com&d=DwIFaQ&c=eLbWYnpnzycBCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJsl0IvoA&m=ujLhFVlRizFeEkHaIJ0lk-QEBm9LowvE-ljMIr1V-o8&s=8eoPW-urqaPARZRE8fkq26gERjoK0kxkhPa7tl_H0HA&e= and include the link in your
> posting.
> > *****
> >
> > Hi Kris
> >
> > It seems from what you are saying, that you knew the PSF spacings
> > were wrong in November but wouldn't confirm it, as not to disrupt
> > the study? I spent many hours in November trouble shooting the
> > ImageJ and Python PSF generators, to see if the issue was with them.
> > It would have been nice to know then that I wasn't going crazy and
> > there weren't bugs in the open source libraries I was using. As a
> > long time contributor to imagej it would have been nice to have
> > reliable test
> images to verify code with.
> >
> > Anyway, why would you have needed to stop the study? All you would
> > have had to do was announce there was a mistake in the PSF and you
> > were working to fix it. In fact it would be interesting to see if
> > you got better or different answers after fixing the PSF.
> >
> > The branding of the study as a reproducibility study is what I am
> > really having an issue with. Reproducibility is a very powerful and
> > personal word to many people, especially people who have experienced
> > real reproducibility controversies and all the horrible politics
> > that go
> with it.
> > Reproducibility is when you try to verify a claim such as 'this
> > method has the best segmentation accuracy", and step by step try to
> > reproduce someone else's work. What you are doing seems to be a
> > variability study. It is certainly valuable but should not be
> > branded as a
> reproducibility study.
> >
> > Brian
> >
> > On Fri, Apr 22, 2022 at 2:46 PM Kubow, Kristopher E - kubowke <
> > [log in to unmask]> wrote:
> >
> > > *****
> > > To join or leave the confocal microscopy listserv or to change
> > > your email address, go to:
> > > https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.umn.edu_cgi-2Dbin_wa-3FSUBED1-3Dconfocalmicroscopy-26A-3D1&d=DwIFaQ&c=eLbWYnpnzycBCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJsl0IvoA&m=ujLhFVlRizFeEkHaIJ0lk-QEBm9LowvE-ljMIr1V-o8&s=Hble3y1wAIBN3iELJ0GtjYGmU61ISQoEdVk9N9tHYnY&e=
> > > Post images on https://urldefense.proofpoint.com/v2/url?u=http-3A__www.imgur.com&d=DwIFaQ&c=eLbWYnpnzycBCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJsl0IvoA&m=ujLhFVlRizFeEkHaIJ0lk-QEBm9LowvE-ljMIr1V-o8&s=8eoPW-urqaPARZRE8fkq26gERjoK0kxkhPa7tl_H0HA&e= and include the link in your
> > posting.
> > > *****
> > >
> > > Hi Brian,
> > >
> > > I agree with the core issue: that there is some kind of mismatch
> > > between the acquisition parameters reported for the nuclei sets
> > > and the PSF apparent in the images and that this may interfere
> > > with deconvolving the image. And I agree that this is an important
> > > issue to resolve. However, I respectfully disagree on the dire
> > > implications of this for our study and event.
> > >
> > > Our study was never intended nor designed to find or rank the best
> > > segmentation procedures. Our goal was simply to assess variability
> > > in the segmentation results produced by a variety of different
> > > people (with different backgrounds/expertise/etc.) using a wide
> variety of approaches.
> > > In this way, our study is very different from the segmentation
> > > challenges that are conducted to crowd-source new and better
> > > algorithms. Although we do hope to make some general conclusions
> > > about what procedures lead to
> > more
> > > or less variability, these conclusions will be very coarse-grained
> > because
> > > they will depend on a sufficient number of people having done the
> > > same operation (which we can't control). For example, it's likely
> > > that many people used some kind of threshold in their procedure,
> > > so we might be
> > able
> > > to make some broad comments on that. Indeed, it would be better to
> > > have a highly controlled experiment (changing just one variable at
> > > a
> > > time) to
> > test
> > > the effects of specific techniques - in particular because
> > > segmentation procedures involve multiple components. Even if we
> > > were to identify everyone who performed deconvolution as an
> > > initial step, they would all likely have different subsequent
> > > steps - all of which might introduce significant variability. Our
> > > primary goal is to assess the current state
> > of
> > > variability (what's currently going on out there in the real
> > > world?) similar to, e.g., the recent study of microscopy methods
> > > reporting by Marques et al. (https://urldefense.proofpoint.com/v2/url?u=https-3A__elifesciences.org_articles_55133&d=DwIFaQ&c=eLbWYnpnzycBCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJsl0IvoA&m=ujLhFVlRizFeEkHaIJ0lk-QEBm9LowvE-ljMIr1V-o8&s=0ht6iY17XbEcPZzcekEmPwSzW0zIUqt3ldWunlcZ6lg&e= ).
> > >
> > > When you brought the PSF issue to our attention several months
> > > ago, we
> > had
> > > to make a decision. At that point, many people had already
> > > completed our study so, in essence, the "damage was done." We
> > > could stop the study,
> > omit
> > > all the previously collected data, identify and fix the problem,
> > > and then start the study from scratch. Or we could continue the
> > > study and accept
> > the
> > > fact that it would be limited in that we would not have
> > > submissions involving deconvolution. Because, to our knowledge,
> > > the PSF problem only affects one potential image operation
> > > (deconvolution) typically involved
> > in
> > > segmentation, and because our study was focused on measuring
> > > overall variability and not the effects of specific techniques, we
> > > decided to continue the study. Now, you might argue whether one
> > > should segment a widefield image without first deconvolving it,
> > > but that's beside the
> > point,
> > > since we are examining not what people ought to do, but what they
> > actually
> > > do. So our study is limited in that people who would have
> > > performed deconvolution before segmenting nuclei may not be
> > > represented in our dataset. We fully admit this limitation, but we
> > > feel that it will not severely impact our broad assessment of
> > > person-to-person variability in image segmentation.
> > >
> > > Likewise, our event next week is not meant to compare the
> > > performance of different programs. It is purely educational: an
> > > opportunity for
> > different
> > > image analysis platforms to demonstrate potential workflows for
> > performing
> > > segmentation and to show the ways that the platform can promote
> > > image analysis reproducibility (e.g. in standardizing and
> > > documenting
> > workflows).
> > > Again, we acknowledge that there is a PSF/deconvolution
> > > limitation, but since that is only one potential element of a
> > > segmentation workflow, we feel that the event will still be
> > > fruitful even if it deconvolution is
> > not
> > > possible.
> > >
> > > Again, we are working with our colleagues at Cytopacq to
> > > understand the problem and will post updates to image.sc. If there
> > > have been any miscommunications or misunderstandings regarding the
> > > study or event's goals, I take full responsibility for that and
> > > hope that I've clarified everything now.
> > >
> > > Best,
> > > -Kris
> > >
> > > ________________________________
> > > From: Brian Northan <[log in to unmask]>
> > > Sent: Wednesday, April 20, 2022 9:28 AM
> > > Subject: Re: 3D Image Analysis Tools and Reproducibility Event -
> > > April 27th via Zoom
> > >
> > > *****
> > > To join or leave the confocal microscopy listserv or to change
> > > your email address, go to:
> > >
> > >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.umn.edu_c
> > gi
> > -2Dbin_wa-3FSUBED1-3Dconfocalmicroscopy-26A-3D1&d=DwIFaQ&c=eLbWYnpnz
> > yc
> > BCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJsl0IvoA&m=WQfBJ5Y4
> > VW
> > f7Nz0nN-nVQLdxVCsinhxexQMO9MQxddA&s=4zdyqyfF4_ngpNFPejYyzhOkqNR1yWoh
> > RJ
> > hmSXPANB4&e=
> > > Post images on
> > >
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.imgur.com&d=
> > Dw
> > IFaQ&c=eLbWYnpnzycBCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJ
> > sl
> > 0IvoA&m=WQfBJ5Y4VWf7Nz0nN-nVQLdxVCsinhxexQMO9MQxddA&s=zjccIXaaAFxbaF
> > yr
> > DAoVgYOIv77ORrUxympimvjBH1c&e=
> > > and include the link in your posting.
> > > *****
> > >
> > > Hi Kris
> > >
> > > ABRF is marketing this workshop and study as 'trying to promote
> > > reproducibility' however in the meantime there is a
> > > reproducibility
> issue
> > > in the study itself that has dragged on for several months. This
> issue
> > > influences algorithm choice. Respectfully, isn't it appropriate
> > > to push hard to have ABRF solve this issue before doing a
> > > reproducibility
> > workshop
> > > next week? If incorrect information, as to appropriate algorithm
> > > choice
> > is
> > > presented in the workshop or study it will take image processing
> > > professionals their time to correct the mistaken impression.
> > >
> > > I understand people at ABRF are busy and I am absolutely not
> > > implying
> > that
> > > ABRF is trying to hide anything, or has intentionally done
> > > anything wrong at all. However, to be honest, I do not think ABRF
> > > (and many other microscopy groups) fully appreciate the types of
> > > technical skills it
> > takes
> > > to do proper justice to complex digital image processing problems.
> > > Oftentimes image processing workshops put on by microscopy groups
> > > are
> > done
> > > in too simple a manner and have led to a lack of rigor in image
> > > processing.
> > >
> > > Brian
> > >
> > >
> > >
> > >
> > > On Tue, Apr 19, 2022 at 1:03 PM Kubow, Kristopher E - kubowke <
> > > [log in to unmask]> wrote:
> > >
> > > > *****
> > > > To join or leave the confocal microscopy listserv or to change
> > > > your
> > email
> > > > address, go to:
> > > >
> > >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.umn.edu_c
> > gi
> > -2Dbin_wa-3FSUBED1-3Dconfocalmicroscopy-26A-3D1&d=DwIFaQ&c=eLbWYnpnz
> > yc
> > BCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJsl0IvoA&m=WQfBJ5Y4
> > VW
> > f7Nz0nN-nVQLdxVCsinhxexQMO9MQxddA&s=4zdyqyfF4_ngpNFPejYyzhOkqNR1yWoh
> > RJ
> > hmSXPANB4&e=
> > > > Post images on
> > >
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.imgur.com&d=
> > Dw
> > IFaQ&c=eLbWYnpnzycBCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJ
> > sl
> > 0IvoA&m=WQfBJ5Y4VWf7Nz0nN-nVQLdxVCsinhxexQMO9MQxddA&s=zjccIXaaAFxbaF
> > yr
> > DAoVgYOIv77ORrUxympimvjBH1c&e=
> > > and include the link in your posting.
> > > > *****
> > > >
> > > > Thanks for your input, Brian - it's much appreciated. And since
> > > > a continued discussion of this sort is more appropriate for
> > > > image.sc,
> > > let's
> > > > move the conversation there. It is better to have the full
> > > > threaded discussion in one place rather than cross-posted to the
> listserv.
> > > >
> > > > Also, I want to emphasize that the study is being conducted by a
> > > > group
> > of
> > > > volunteers in our "spare time." All of us run core facilities -
> > > > many of
> > > us
> > > > completely by ourselves (no staff). Many of us also teach and/or
> > > > have
> > > other
> > > > obligations at our institutions. None of us are paid/compensated
> > (either
> > > by
> > > > our institutions or the ABRF) to run the study. We are in no way
> > > > trying
> > > to
> > > > hide anything. We are trying to do our best within our
> > > > constraints. I understand you wish things would move more
> > > > quickly (so do we!), but
> > even
> > > > tasks that might seem to be straightforward/quick/obvious/etc.
> > > > do take
> > > time
> > > > and require coordination among our members. I don't say this to
> > > > be confrontational or condescending, but only to emphasize that
> > > > our
> > members
> > > > are well-meaning, hard-working individuals who are trying to do
> > > > their
> > > best
> > > > with what they have.
> > > >
> > > > I look forward to engaging with you further on the deconvolution
> > > > issue
> > at
> > > > image.sc.
> > > >
> > > > Best,
> > > > -Kris
> > > >
> > > > ________________________________
> > > > From: Brian Northan <[log in to unmask]>
> > > > Sent: Monday, April 18, 2022 8:12 AM
> > > > Subject: Re: 3D Image Analysis Tools and Reproducibility Event -
> > > > April 27th via Zoom
> > > >
> > > > *****
> > > > To join or leave the confocal microscopy listserv or to change
> > > > your
> > email
> > > > address, go to:
> > > >
> > > >
> > >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.umn.edu_c
> > gi
> > -2Dbin_wa-3FSUBED1-3Dconfocalmicroscopy-26A-3D1&d=DwIFaQ&c=eLbWYnpnz
> > yc
> > BCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJsl0IvoA&m=lMiutr1d
> > y6
> > jxfbZfb00NtOJHkGisOXchgySLZr_ltdM&s=qG6OzlR17xLhXVpo66_yZ3GUTqte32xr
> > V4
> > awF3aiY3k&e=
> > > > Post images on
> > > >
> > >
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.imgur.com&d=
> > Dw
> > IFaQ&c=eLbWYnpnzycBCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJ
> > sl
> > 0IvoA&m=lMiutr1dy6jxfbZfb00NtOJHkGisOXchgySLZr_ltdM&s=tCrWXALdZYlJ-B
> > Hr
> > rWfqDrabDddXGFqbajpsBYTjJN0&e=
> > > > and include the link in your posting.
> > > > *****
> > > >
> > > > Thanks Kris
> > > >
> > > > Just to re-emphasize why this issue is so important. To get
> > > > accurate intensities and segmentation of the nuclei images some
> > > > type of image restoration must be done (either deconvolution or
> > > > AI based
> > restoration).
> > > > The segmentations I've seen of the nuclei image, so far, looked
> > > > good
> > at
> > > > first glance (round well separated objects), however are merely
> > > > simplifications which fit a spheroid to the data, but do not
> > > > capture
> > the
> > > > true shape or intensities.
> > > >
> > > > Anyway, I will spend some time this week or next looking over
> > > > the
> > docker
> > > > release and see if I can tell what happened with the PSF. Seems
> > > > like
> > it
> > > is
> > > > probably a resampling issue, perhaps even as simple as incorrect
> > reading
> > > of
> > > > spacings from the meta-data, but hard to know for sure.
> > > >
> > > > Brian
> > > >
> > > > Brian
> > > >
> > > > On Sun, Apr 17, 2022 at 8:08 PM Kubow, Kristopher E - kubowke <
> > > > [log in to unmask]> wrote:
> > > >
> > > > > *****
> > > > > To join or leave the confocal microscopy listserv or to change
> > > > > your
> > > email
> > > > > address, go to:
> > > > >
> > > >
> > >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.umn.edu_c
> > gi
> > -2Dbin_wa-3FSUBED1-3Dconfocalmicroscopy-26A-3D1&d=DwIFaQ&c=eLbWYnpnz
> > yc
> > BCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJsl0IvoA&m=lMiutr1d
> > y6
> > jxfbZfb00NtOJHkGisOXchgySLZr_ltdM&s=qG6OzlR17xLhXVpo66_yZ3GUTqte32xr
> > V4
> > awF3aiY3k&e=
> > > > > Post images on
> > > >
> > >
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.imgur.com&d=
> > Dw
> > IFaQ&c=eLbWYnpnzycBCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJ
> > sl
> > 0IvoA&m=lMiutr1dy6jxfbZfb00NtOJHkGisOXchgySLZr_ltdM&s=tCrWXALdZYlJ-B
> > Hr
> > rWfqDrabDddXGFqbajpsBYTjJN0&e=
> > > > and include the link in your posting.
> > > > > *****
> > > > >
> > > > > Question was cross-posted on image.sc forum please see forum
> > > > > for
> > > > response
> > > > > and continuation of discussion:
> > > > >
> > > >
> > >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__forum.image.sc_
> > t_
> > 3d-2Dimage-2Danalysis-2Dtools-2Dand-2Dreproducibility-2Devent-2Dapri
> > l-
> > 2D27th-2Dvia-2Dzoom_64671_5-3Fu-3Dkris-5Fkubow&d=DwIFaQ&c=eLbWYnpnzy
> > cB
> > Cgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJsl0IvoA&m=lMiutr1dy
> > 6j
> > xfbZfb00NtOJHkGisOXchgySLZr_ltdM&s=-Y-XonaNJ5KjpvnIEH1yhfrJANHJuRnQq
> > U1
> > 5_lCOqxs&e=
> > > > >
> > > > > ________________________________
> > > > > From: Brian Northan <[log in to unmask]>
> > > > > Sent: Friday, April 15, 2022 6:09 AM
> > > > > Subject: Re: 3D Image Analysis Tools and Reproducibility Event
> > > > > -
> > April
> > > > > 27th via Zoom
> > > > >
> > > > > *****
> > > > > To join or leave the confocal microscopy listserv or to change
> > > > > your
> > > email
> > > > > address, go to:
> > > > >
> > > > >
> > > >
> > >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.umn.edu_c
> > gi
> > -2Dbin_wa-3FSUBED1-3Dconfocalmicroscopy-26A-3D1&d=DwIFaQ&c=eLbWYnpnz
> > yc
> > BCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJsl0IvoA&m=hBsapqAz
> > r5
> > hAx-G9-qM3LSc9TEwTGgBoh0n4rbwkBks&s=z0i7P1WXTT-6ZCuw6KqHreKuHf-jiYoJ
> > TF
> > fEJo1rass&e=
> > > > > Post images on
> > > > >
> > > >
> > >
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.imgur.com&d=
> > Dw
> > IFaQ&c=eLbWYnpnzycBCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJ
> > sl
> > 0IvoA&m=hBsapqAzr5hAx-G9-qM3LSc9TEwTGgBoh0n4rbwkBks&s=wPbLmuOcWhpfci
> > V0
> > CceO3Wq0xE9rQgqBl5U33Gian8E&e=
> > > > > and include the link in your posting.
> > > > > *****
> > > > >
> > > > > Hi Kris
> > > > >
> > > > > Any update on this? Why not just release the forward model
> > > > > code
> > > > publically
> > > > > and have the community look it over? I don't understand how
> > > > > ABRF can
> > > > claim
> > > > > they are addressing 'reproducibility' when they are working in
> > > > > such a closed manner. Isn't openness and communication the
> > > > > number one
> > > principle
> > > > > of reproducibility?
> > > > >
> > > > > Brian
> > > > >
> > > > > On Thu, Mar 24, 2022 at 3:28 PM Kubow, Kristopher E - kubowke
> > > > > < [log in to unmask]> wrote:
> > > > >
> > > > > > *****
> > > > > > To join or leave the confocal microscopy listserv or to
> > > > > > change your
> > > > email
> > > > > > address, go to:
> > > > > >
> > > > >
> > > >
> > >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.umn.edu_c
> > gi
> > -2Dbin_wa-3FSUBED1-3Dconfocalmicroscopy-26A-3D1&d=DwIFaQ&c=eLbWYnpnz
> > yc
> > BCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJsl0IvoA&m=hBsapqAz
> > r5
> > hAx-G9-qM3LSc9TEwTGgBoh0n4rbwkBks&s=z0i7P1WXTT-6ZCuw6KqHreKuHf-jiYoJ
> > TF
> > fEJo1rass&e=
> > > > > > Post images on
> > > > >
> > > >
> > >
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.imgur.com&d=
> > Dw
> > IFaQ&c=eLbWYnpnzycBCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJ
> > sl
> > 0IvoA&m=hBsapqAzr5hAx-G9-qM3LSc9TEwTGgBoh0n4rbwkBks&s=wPbLmuOcWhpfci
> > V0
> > CceO3Wq0xE9rQgqBl5U33Gian8E&e=
> > > > > and include the link in your posting.
> > > > > > *****
> > > > > >
> > > > > > Thanks Brian and David. We agree that there does seem to be
> > > > > > a
> > > mismatch
> > > > > > between the spacing parameters that were given and what is
> > > > > > actually
> > > > used
> > > > > in
> > > > > > the nuclei images. This will impact deconvolution of the
> > > > > > images, if
> > > > > people
> > > > > > elect to do that as part of their segmentation protocol for
> > > > > > the
> > > study.
> > > > > > We’re currently looking into the problem and are in contact
> > > > > > with
> > the
> > > > > group
> > > > > > that developed the simulation software. We'll post updates
> > > > > > (when we
> > > get
> > > > > > them) on the image.sc forum:
> > > > > >
> > > > >
> > > >
> > >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__forum.image.sc_
> > t_
> > 3d-2Dimage-2Danalysis-2Dtools-2Dand-2Dreproducibility-2Devent-2Dapri
> > l-
> > 2D27th-2Dvia-2Dzoom_64671&d=DwIFaQ&c=eLbWYnpnzycBCgmb7vCI4uqNEB9RSjO
> > dn
> > _5nBEmmeq0&r=wgGHXpNkPeE6PJJsl0IvoA&m=hBsapqAzr5hAx-G9-qM3LSc9TEwTGg
> > Bo h0n4rbwkBks&s=SMse04bgkg546B_NFjehOds-hRMIW4bovk4mbCxMeqc&e=
> > > > > >
> > > > > > ________________________________
> > > > > > From: Brian Northan <[log in to unmask]>
> > > > > > Sent: Wednesday, March 23, 2022 9:26 AM
> > > > > > Subject: Re: 3D Image Analysis Tools and Reproducibility
> > > > > > Event
> > > > > > -
> > > April
> > > > > > 27th via Zoom
> > > > > >
> > > > > > *****
> > > > > > To join or leave the confocal microscopy listserv or to
> > > > > > change your
> > > > email
> > > > > > address, go to:
> > > > > >
> > > > > >
> > > > >
> > > >
> > >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.umn.edu_c
> > gi
> > -2Dbin_wa-3FSUBED1-3Dconfocalmicroscopy-26A-3D1&d=DwIFaQ&c=eLbWYnpnz
> > yc
> > BCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJsl0IvoA&m=Bbo8EpRK
> > zd
> > BsReltSfbg8Udr6_-vbdBTWzo2_VmZUow&s=-owGyRKzOtmTtqOXx9hHPa81IsG5cCt5
> > iC
> > VjWV4ILTg&e=
> > > > > > Post images on
> > > > > >
> > > > >
> > > >
> > >
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.imgur.com&d=
> > Dw
> > IFaQ&c=eLbWYnpnzycBCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJ
> > sl
> > 0IvoA&m=Bbo8EpRKzdBsReltSfbg8Udr6_-vbdBTWzo2_VmZUow&s=uQ0i7zYMybxCqH
> > 94
> > JEtgiMLq5Tqf4RT45jB8kGVrshU&e=
> > > > > > and include the link in your posting.
> > > > > > *****
> > > > > >
> > > > > > Interestingly I used similar spacings to those David estimated.
> > > After
> > > > > > first using the given spacings and getting terrible
> > > > > > deconvolution
> > > > > results,
> > > > > > I simply used the Nyquist spacings and got a much better result.
> > > > > > From there I tweaked the spacings a bit and used 0.1 XY and
> > > > > > 0.8 Z
> > and
> > > > > got a
> > > > > > pretty good deconvolution.
> > > > > >
> > > > > > I mentioned this to Kris Kublow, one of the organizers
> > > > > > several
> > months
> > > > ago
> > > > > > and he said the group would look into it, but I never heard
> > > > > > if they
> > > > did.
> > > > > >
> > > > > > Jessica, did your group ever run tests to validate the PSF,
> > > > > > forward
> > > > model
> > > > > > and spacings? If so, how did you convince yourself the
> > > > > > simulation
> > > was
> > > > > > correct?
> > > > > >
> > > > > > Brian
> > > > > >
> > > > > >
> > > > > > On Mon, Mar 21, 2022 at 1:09 PM David Biggs
> > > > > > <[log in to unmask]>
> > > > wrote:
> > > > > >
> > > > > > > *****
> > > > > > > To join or leave the confocal microscopy listserv or to
> > > > > > > change
> > your
> > > > > email
> > > > > > > address, go to:
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.umn.edu_c
> > gi
> > -2Dbin_wa-3FSUBED1-3Dconfocalmicroscopy-26A-3D1&d=DwIFaQ&c=eLbWYnpnz
> > yc
> > BCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJsl0IvoA&m=Bbo8EpRK
> > zd
> > BsReltSfbg8Udr6_-vbdBTWzo2_VmZUow&s=-owGyRKzOtmTtqOXx9hHPa81IsG5cCt5
> > iC
> > VjWV4ILTg&e=
> > > > > > > Post images on
> > > > > >
> > > > >
> > > >
> > >
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.imgur.com&d=
> > Dw
> > IFaQ&c=eLbWYnpnzycBCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJ
> > sl
> > 0IvoA&m=Bbo8EpRKzdBsReltSfbg8Udr6_-vbdBTWzo2_VmZUow&s=uQ0i7zYMybxCqH
> > 94
> > JEtgiMLq5Tqf4RT45jB8kGVrshU&e=
> > > > > > and include the link in your posting.
> > > > > > > *****
> > > > > > >
> > > > > > > In reference to Brian's observations, I also concur that
> > > > > > > the
> > > > parameters
> > > > > > > provided for the widefield nuclei dataset do not match the
> > > > > > > data
> > > > > provided.
> > > > > > > For a 0.75 NA air lens, I estimate the Z spacing is closer
> > > > > > > to
> > > 0.75um,
> > > > > and
> > > > > > > the XY spacing is closer to 0.1um.
> > > > > > > I roughly estimated these from the shape of the missing
> > > > > > > cone in
> > the
> > > > > > Fourier
> > > > > > > domain.
> > > > > > >
> > > > > > > Any clarification would be appreciated.
> > > > > > >
> > > > > > > Thanks,
> > > > > > > David
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > On Sat, Mar 19, 2022 at 1:44 PM Brian Northan <
> > [log in to unmask]>
> > > > > > wrote:
> > > > > > >
> > > > > > > > *****
> > > > > > > > To join or leave the confocal microscopy listserv or to
> > > > > > > > change
> > > your
> > > > > > email
> > > > > > > > address, go to:
> > > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.umn.edu_c
> > gi
> > -2Dbin_wa-3FSUBED1-3Dconfocalmicroscopy-26A-3D1&d=DwIFaQ&c=eLbWYnpnz
> > yc
> > BCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJsl0IvoA&m=Bbo8EpRK
> > zd
> > BsReltSfbg8Udr6_-vbdBTWzo2_VmZUow&s=-owGyRKzOtmTtqOXx9hHPa81IsG5cCt5
> > iC
> > VjWV4ILTg&e=
> > > > > > > > Post images on
> > > > > >
> > > > >
> > > >
> > >
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.imgur.com&d=
> > Dw
> > IFaQ&c=eLbWYnpnzycBCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJ
> > sl
> > 0IvoA&m=Bbo8EpRKzdBsReltSfbg8Udr6_-vbdBTWzo2_VmZUow&s=uQ0i7zYMybxCqH
> > 94
> > JEtgiMLq5Tqf4RT45jB8kGVrshU&e=
> > > > > > and include the link in your
> > > > > > > posting.
> > > > > > > > *****
> > > > > > > >
> > > > > > > > Has anyone else tried to deconvolve the nuclei images
> > > > > > > > used in
> > the
> > > > > > > study? I
> > > > > > > > was only able to obtain a good deconvolution result
> > > > > > > > after
> > > > > introducing a
> > > > > > > > fudge factor into the PSF generation. Is anybody else
> > > > > > > > running
> > > into
> > > > > the
> > > > > > > > same problem? My concern is that there is a potential
> > > > > > > > sampling
> > > > issue
> > > > > > in
> > > > > > > > the PSF used in the simulation, and that in turn could
> > (falsely)
> > > > make
> > > > > > it
> > > > > > > > seem as if deconvolution doesn't work. That would be a
> > > > > > > > shame, deconvolution is an important tool for processing
> > > > > > > > 3D Widefield
> > > > > > > fluorescence
> > > > > > > > images, and it would be nice if this study could be
> > > > > > > > used, to
> > > > > > demonstrate
> > > > > > > > the benefits of deconvolution.
> > > > > > > >
> > > > > > > > Contact me off list if you would like. I'd like to
> > > > > > > > verify that
> > > > these
> > > > > > > > images can be deconvolved using standard tools.
> > > > > > > >
> > > > > > > > Brian
> > > > > > > >
> > > > > > > > On Fri, Mar 18, 2022 at 9:44 AM Jessica Hornick <
> > > > > > > > [log in to unmask]>
> > > > > > > > wrote:
> > > > > > > >
> > > > > > > > > *****
> > > > > > > > > To join or leave the confocal microscopy listserv or
> > > > > > > > > to
> > change
> > > > your
> > > > > > > email
> > > > > > > > > address, go to:
> > > > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.umn.edu_c
> > gi
> > -2Dbin_wa-3FSUBED1-3Dconfocalmicroscopy-26A-3D1&d=DwIFaQ&c=eLbWYnpnz
> > yc
> > BCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJsl0IvoA&m=Bbo8EpRK
> > zd
> > BsReltSfbg8Udr6_-vbdBTWzo2_VmZUow&s=-owGyRKzOtmTtqOXx9hHPa81IsG5cCt5
> > iC
> > VjWV4ILTg&e=
> > > > > > > > > Post images on
> > > > > >
> > > > >
> > > >
> > >
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.imgur.com&d=
> > Dw
> > IFaQ&c=eLbWYnpnzycBCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJ
> > sl
> > 0IvoA&m=Bbo8EpRKzdBsReltSfbg8Udr6_-vbdBTWzo2_VmZUow&s=uQ0i7zYMybxCqH
> > 94
> > JEtgiMLq5Tqf4RT45jB8kGVrshU&e=
> > > > > > and include the link in your
> > > > > > > > posting.
> > > > > > > > > *****
> > > > > > > > >
> > > > > > > > > Come learn more about 3D image analysis tools and how
> > > > > > > > > they
> > can
> > > > help
> > > > > > > > > improve reproducibility at this two-hour online
> > > > > > > > > workshop
> > hosted
> > > > by
> > > > > > the
> > > > > > > > > Light Microscopy Research Group of the ABRF!
> > > > > > > > >
> > > > > > > > > This event will be centered around the LMRG’s ongoing
> > > > > > > > > study
> > of
> > > > > > > > > reproducibility in 3D image analysis in which we seek
> > > > > > > > > to
> > > > > characterize
> > > > > > > and
> > > > > > > > > identify sources of (ir)reproducibility in 3D segmentation.
> > Try
> > > > > your
> > > > > > > hand
> > > > > > > > > at analyzing the study images and then attend the
> > > > > > > > > workshop to
> > > see
> > > > > how
> > > > > > > the
> > > > > > > > > pros would do it. Representatives from several major
> > > > > > > > > 3D
> > > analysis
> > > > > > > > platforms
> > > > > > > > > will walk attendees through how to segment and analyze
> > > > > > > > > the
> > > images
> > > > > > from
> > > > > > > > our
> > > > > > > > > study and will discuss how their platforms support
> > reproducible
> > > > > image
> > > > > > > > > analysis. These demonstrations will occur
> > > > > > > > > simultaneously in
> > > > > breakout
> > > > > > > > rooms
> > > > > > > > > and attendees may choose up to two to attend. There
> > > > > > > > > will also
> > > be
> > > > an
> > > > > > > open
> > > > > > > > > session at the conclusion of the program during which
> > attendees
> > > > may
> > > > > > > visit
> > > > > > > > > and talk with any representative they like. Note that
> > > > > > > > > the
> > > > platforms
> > > > > > > will
> > > > > > > > > not be competing against each other–the purposes of
> > > > > > > > > the event
> > > are
> > > > > > > > > instructional/informational and to promote
> > > > > > > > > reproducibility in
> > > > image
> > > > > > > > > analysis.
> > > > > > > > >
> > > > > > > > > We will host representatives from the following platforms:
> > > > > > ImageJ/FIJI,
> > > > > > > > > Napari, CellProfiler, Arivis, and Volocity. We hope to
> > > > > > > > > add
> > more
> > > > to
> > > > > > this
> > > > > > > > > list before the event.
> > > > > > > > >
> > > > > > > > > The event will take place on April 27th at 8:00 am
> > > > > > > > > Pacific
> > > Time /
> > > > > > 11:00
> > > > > > > > am
> > > > > > > > > Eastern Time via Zoom.
> > > > > > > > >
> > > > > > > > > ** Register for the event here:
> > > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__us02web.zoom.us
> > _m
> > eeting_register_tZEsceuvpzIvH9e0kFHEuWdxRMBAgrrpUwzj&d=DwIFaQ&c=eLbW
> > Yn
> > pnzycBCgmb7vCI4uqNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJsl0IvoA&m=Bbo
> > 8E
> > pRKzdBsReltSfbg8Udr6_-vbdBTWzo2_VmZUow&s=df5s8P1S7R061gnHC6OXrqAOlhV
> > J3
> > FaJP5Wt8KsC0Qo&e=
> > > > > > > > >
> > > > > > > > > This event is targeted to people who are interested in
> > learning
> > > > > more
> > > > > > > > about
> > > > > > > > > a specific image analysis platform, learning how to
> > > > > > > > > use an
> > > image
> > > > > > > analysis
> > > > > > > > > tool better, and/or learning about how reproducibility
> > > > > > > > > is
> > > > addressed
> > > > > > by
> > > > > > > > > these platforms.
> > > > > > > > >
> > > > > > > > > We strongly encourage attendees to participate in the
> > > > > > > > > study
> > > > before
> > > > > > the
> > > > > > > > > event so that you are familiar with the image analysis
> > problem.
> > > > > > > Attendees
> > > > > > > > > who participate in the study before the event will be
> > > > > > > > > entered
> > > in
> > > > a
> > > > > > $50
> > > > > > > > > Amazon gift card drawing. (If you’ve already
> > > > > > > > > participated in
> > > the
> > > > > > study
> > > > > > > > and
> > > > > > > > > didn’t win in our last drawing, you’re automatically
> > entered.)
> > > > > Study
> > > > > > > info
> > > > > > > > > can be found here:
> > > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__sites.google.co
> > m_
> > view_lmrg-2Dimage-2Danalysis-2Dstudy&d=DwIFaQ&c=eLbWYnpnzycBCgmb7vCI
> > 4u
> > qNEB9RSjOdn_5nBEmmeq0&r=wgGHXpNkPeE6PJJsl0IvoA&m=Bbo8EpRKzdBsReltSfb
> > g8
> > Udr6_-vbdBTWzo2_VmZUow&s=AvCI1kJRHZzgNZUP-7MfZJdOZZaCKUJOvPZAamulY-0
> > &e
> > =
> > > > > > > > >
> > > > > > > > > If you have questions about the event, please contact
> > > > > > > > > Jessica
> > > > > > Hornick (
> > > > > > > > > [log in to unmask]).
> > > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> --
> ________________________________________
>
> Dr. Thomas Pengo
> Director of Applications and Services, UMII University of Minnesota,
> Twin Cities Campus Cancer and Cardiovascular Research Building
> 2231 6th St SE
> Minneapolis, MN 55455
>
|
