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High-Throughput Truthing (HTT) Update

 

Link to the details of this update, including:

  •   High-Throughput Truthing (HTT) Project Update
    • Pitch: We are launching a project to crowdsource pathologists and collect data (images + pathologist annotations) that can be qualified by the FDA/CDRH medical device development tool program (MDDT). The MDDT qualified data would be available to any algorithm developer to be used to validate their algorithm performance in a submission to the FDA/CDRH.
  •   HTT Project Call for Collaboration
  •   Quick info about FDA submissions for medical imaging algorithms
     

Link to full list of HTT updates

Link to full list of eeDAP updates

 

cheers,

the eeDAP team

353

Subject of this announcement:

  • Request for 3D WSI image needing segmentation
  • New manuscript by Brandon highlighting multiple-reader, multiple-case study design and analysis
  • Short update on HTT project

Request for 3D WSI needing segmentation: My colleagues have started building a research area around augmented reality, virtual reality, and medical imaging devices. They are looking for 3D WSIs that they can use in their research to investigate a registration task. If you know of any publicly available data (or easily shared), we would really like to know.

New manuscript: A few of you have suggested that the group might like to see a recent publication by my colleagues and I: “Impact of prevalence and case distribution in lab-based diagnostic imaging studies,” (doi: 10.1117/1.JMI.6.1.015501). There were five lab-based studies with study populations that differed in terms of breast cancer prevalence and the distribution of non-cancer patients (screening vs. challenging). Twenty radiologists participated in each study. The studies demonstrated modern methods in study design, data collection, and analysis tools that offer improvements in terms of statistical efficiency and data quality. Supplementary materials, including the data and analysis scripts, are available at https://github.com/DIDSR/viperData.

I'll also take this moment to share a paper by my colleagues that others have also asked about, "Evaluation of Digital Breast Tomosynthesis as Replacement of Full-Field Digital Mammography Using an In Silico Imaging Trial." I hope you enjoy it.

Short update on HTT project: We are going through some growing pains as we figure out how to structure the project, leverage the contributions people have volunteered, and start moving forward. Often, the glue for holding a project together is handled within the structure of a grant or some research agreement. Whatever the mechanism, we are drafting more detail on the deliverables, tasks, and timeline. The goal is to distribute the effort and provide structure for people to participate and contribute. Additionally, we will be pursuing funding. We hope to provide an update soon and start having regular T-cons.

348

How does a government employee address collaborators and friends during a shutdown?
I have no idea. I don’t even know how to respond to the simplest questions like, “How’s it going?”

 

Anyhow, after many weeks of being furloughed I have been recently designated as “partially exempt”. I am allowed to work on regulatory consults and already submitted Medical Device Development Tools (MDDTs). In particular, I can work on the eeDAP MDDT! The eeDAP MDDT has been languishing thanks to other deadlines and new work. Now it is at the top of my to-do pile.

 

We are looking for feedback on the MDDT inquiry to the FDA. Please send me comments or ask for an extension by the morning of Monday 11-Feb-2019.

 

Regarding the HTT work, while the sales pitch for the CP project proposal was about creating MDDT datasets, many of you know the project origins were to explore and demonstrate the role that eeDAP can play in the regulatory process. Specifically, the planned data-collection events would explore and demonstrate eeDAP regulatory use cases: to use a microscope to collect reference evaluations that can be compared to evaluations using the digital WSIs or to evaluations from algorithms. As such, we are going to proceed with the data-collection events and postpone the work that would create MDDT data sets until after the shutdown.

 

What’s the status of HTT work, the data-collection events?

  • We have identified providers of glass slides and images.
  • We have identified caMicroscope and the Cancer Imaging Archive as the infrastructure to be used for WSI annotations. WSI annotations are needed for study prep and data collection in digital mode.
  • We have outlined drafts of the study prep and data collection workflows.
  • We have identified several events where we can conduct the reader studies.

What needs to get done?

  • Establish IRBs and agreements to govern the sharing of slides and images and to allow for the data collection.
  • Set up and test infrastructure.
  • Develop study prep and data collection workflows.
  • We will miss the opportunity to conduct a data-collection event at USCAP (local for FDA in 2019). No money. No prep. So sad. That said, we now have a little breathing room to work out the IRBs and agreements.

 

Thanks for your attention. I’m so sorry that I have not been responsive to emails. I’m not supposed to work on them if they don’t fall within the scope of my exempted duties. I hope you understand.

Brandon D. Gallas, PhD

Mathematician
Division of Imaging, Diagnostics, and Software Reliability (DIDSR)
Office of Science and Engineering Laboratories (OSEL)
Center for Devices and Radiological Health (CDRH)

10903 New Hampshire Ave, WO-62 Rm 4104, Silver Spring, MD 20993
Email: brandon.gallas@fda.hhs.gov
Phone: 301-796-2531

347

Hello everyone.

Here is a link to the slides that Brandon presented to members of this group: an overview of the project:
 * [https://nciphub.org/groups/eedapstudies/wiki/HighthroughputTruthingYear2/File:20181130-HTToverviewToCollabs.pdf]

Roberto Salgado has invited Brandon to present to the [http://www.tilsinbreastcancer.org] working group face-to-face meeting attached to the San Antonio Breast Cancer. The presentation will largely be the overview linked above.
 *Thursday,  December 6, 2018, 7am-9am (EST).

Ashish Sharma will give an Overview of QuIP/caMicroscope and the TCIA pathology capabilities. We will harness these tools in the HTT project so humans and algorithms can annotate the images via web-based apps to prepare our studies.
 * Monday, December 10, 2018, 11am-12pm (EST)
 * WebEx info below abstract.

Abstract: An overview of QuIP/caMicroscope and the TCIA pathology capabilities. This includes image management, visualization, cloud computing, human/machine annotation and markup and the dissemination of this data. We can also discuss the scope, scale and capabilities of our various digital pathology research activities, including our collaboration with the SEER program.   
 
Join Webex meeting   
 * [https://fda1.webex.com/fda1/j.php?MTID=mbee218a10bec84c095027f6958df8a34]

Meeting number (access code): 901 145 661
Meeting password: mUHY7am2  
 
Join by phone  
+1-210-795-0506 US Toll  
+1-877-465-7975 US Toll Free  
Global call-in numbers  
 * [https://fda1.webex.com/fda1/globalcallin.php?serviceType=MC&ED=10036292&tollFree=1]

Toll-free calling restrictions  
 * [https://e-meetings.verizonbusiness.com/global/pdf/Verizon_Audio_Conferencing_Global_Access_Information_August2017.pdf]
 
Can't join the meeting?
 * [https://collaborationhelp.cisco.com/article/WBX000029055]
 
IMPORTANT NOTICE: Please note that this Webex service allows audio and other information sent during the session to be recorded, which may be discoverable in a legal matter. By joining this session, you automatically consent to such recordings. If you do not consent to being recorded, discuss your concerns with the host or do not join the session.

341

This announcement is identical to the one that I sent to the WSI WG. I apologize if you get both, but I know some of you are not in that group (but I wish you were ... go join it ... https://nciphub.org/groups/wsi_working_group).

 

Summer is over, the new fiscal year is started (for the US gov), and we are planning our next year of research in FDA’s Office of Science and Engineering Laboratories, and hopefully in collaboration with members of the WSI WG community. A reminder here is that OSEL is the research arm of CDRH and does not necessarily reflect any specific policy/decision making of CDRH’s regulatory offices (OIR or ODE).

 * Brandon Gallas will give a '''!WebEx reprise of his presentation''' given at the European Congress of Pathology on 9 September 2018
    * “Evaluating Computational Pathology at the US FDA and Related Research.” (Link to presentation.)
    * !WebEx Date and Time: '''Thursday at 11am on 11 October 2018''' (Link to WebEx info.)

 * In addition to the ECP presentation, I plan to summarize my research plans for the coming year.  Primarily, I plan to collect data (images and annotations) and propose it to be qualified by the FDA/CDRH as a Medical Device Development Tool (MDDT) to be used in submissions to the FDA to validate algorithms.  I will also outline other WSI- and algorithm-related projects by other investigators in my division:
    * Marios Gavrielides plans to examine issues related to the stand-alone assessment of computer-aided diagnosis systems for primary diagnosis, with an application to ovarian cancer subtyping.
    * Anant Agrawal plans to develop a phantom for technical assessment of WSI systems using nanoscale 3D printing.
    * Berkman Sahiner and Weijie Chen plan to expand the evaluation of artificial intelligence and machine learning devices to less structured post-market reference standards and higher risk/higher impact autonomous use.

 * Brandon Gallas is conducting a '''pilot reader study''' at the Annual Meeting of the American Society of Clinical Pathologists in '''Baltimore on 3-5 October 2018.'''
    * This pilot is to support the data MDDT project mentioned above.
    * The pathologists’ tasks are to evaluate lymphocytes in lung tumors.
    * Come find the booth, hear about the study, and participate!
    * We hope to follow up the pilot with a pivotal study at the San Antonio Breast Cancer Symposium or other venue with many pathologists. If you are a conference organizer or are leadership in a professional society and want to help make this happen, please contact Brandon.

 * Check out, “Advancing Regulatory Science with Computational Modeling for Medical Devices at the FDA’s Office of Science and Engineering Laboratories” (Link to paper.). You will be surprised by what is happening at the FDA.

 * Enough of Brandon and FDA-related research, it’s time to hear from the WSI WG. What are you doing? What are your concerns? What discussions and collaborations should we be having? Several WSI WG members have asked what happened to the discussions about using phantoms for the technical performance assessment of WSI scanners, especially as image quality impacts training and testing in computational pathology.
    * '''How should we leverage and engage the 145 WSI WG members?'''
    * Please send co-committee member Marios Gavrielides ideas (Marios.Gavrielides@fda.hhs.gov). He will summarize the feedback that he receives and plan future discussions.

328

Hi All,

 

Some of you know that I presented at the Computational Pathology Workshop at the European Congress of Pathology last week. I wanted to share my slides with you. They discuss the evaluation of image-based algorithms at the FDA, research from the last year, and my research plans. These plans include the development of use cases and validation data (images plus annotations). I’m drafting a project proposal for internal funding that I will also share in the near future … it is due Oct. 19. Hopefully some of you might be interested in collaborating.

 

Anyhow, below is a blurb that I have been sharing with people that have followed up with me after the conference. It includes a link to the slides.

-

Thanks for asking about my work. I’m glad you are interested. Let me first invite you to join the WSI working group (https://nciphub.org/groups/wsi_working_group). It is open to anyone and free. I push info to this group from time to time: relevant FDA information, upcoming meetings, and other scientific events and information (check out the blog). Don’t worry, though, the emails don’t come very often (Iess than 1 per month on average). I don’t want your cranial neural network to flag the emails as spam. In order to join the group, you’ll have to create an account at https://NCIPhub.org (an NCI funded collaboratory portal for cancer research). So you know, if you are doing cancer related research, you can create your own groups and projects on NCIPhub. Thank you to the U.S. National Cancer Informatics Program!

 

You can find my slides from the European Congress of Pathology in the WSIWG wiki. Here is the link: https://nciphub.org/groups/wsi_working_group/wiki/Presentation:Gallas2018_ECP

 

I intend to send an announcement about the slides to the WSIWG soon and present them again as a WebEx. If you are a member of the WSIWG, you will get this announcement and the information for the WebEx. Since some of you asked for more information on our work (reader studies and WSI technical performance), I am talking with my colleagues about sharing our FY2019 internal funding proposals that we are drafting now. This will be a good opportunity for feedback or to collaborate.

324

Is everyone as busy as I feel? Isn’t summer supposed to be relaxing?

My colleague and mentor Bob Wagner always called it the curse of modern life.

 

Anyhow, I have updated the wiki page for our project. In particular, I have uploaded the FY2018-Q3 project report that I submitted to the FDA office in charge of the Critical Path funding mechanism.

https://nciphub.org/groups/eedapstudies/wiki/HighThroughputTruthing

 

To be clear, this is an update for listed collaborators and beyond. This is being posted to the NCIPhub eeDAP studies group, which is open to the public. I will ultimately point the WSI working group to this update as well. Thank you for being in the NCIPhub eeDAP studies group.

 

Generally, things are moving. I would be very happy to make similar progress in the next quarter. Now there are some necessary logistical things that have started and need to continue to move forward (MTAs, CRADAs, etc), and there also are some interesting and fun science coming our way (studies to design and execute). Please refer to wiki page and the FY2018-Q3 report. I am very appreciative of the support received so far and hope y’all will continue to help moving forward. I’d like to convene a Tcon early August to review this update with everyone to answer questions and get feedback. So please review and make some notes and feel free to email me with questions or feedback in the meantime.

 

All the best,

Brandon

321

Hey all,

 

This is a duplicate of the announcement I’m making on the NCIPhub. Remember, I’d like to centralize our communications to the hub. Please join the group there … https://nciphub.org/groups/eedapstudies

 

Quickly, I’d like to give myself a deadline for sharing progress on analyzing the eeDAP studies conducted at MSKCC.

Yukako et al., Can we get a critical mass of your group on a T-con Wed. 5/2? What time?

 

Below I’m sharing some interesting related technologies with exciting clinical applications. I could also imagine some powerful studies if integrated with eeDAP.

Yukako et al., Can you ask their Olympus rep if we can attach this to the multi-head microscope so all the pathologists see the in-microscope-eyepiece display?

 

Augmentiqs: http://journals.sagepub.com/doi/pdf/10.1177/0192623317743722

Google: https://research.googleblog.com/2018/04/an-augmented-reality-microscope.html

 

Brandon

 

 

From: Gallas, Brandon D.
Sent: Thursday, March 29, 2018 3:32 PM
To: sirintrs@mskcc.org
Subject: RE: PI abstract - novel method for automated data acquisition

 

We are sharing the eeDAP technology liberally. Everything is in the public domain. Our goal is to improve public health.

 

The technology described in the abstract is telepathology: from a remote location, you can see the same field of view as the microscope. The device is modular so it appears to work with any microscope (pretty cool), it covers the entire FOV (not such a huge deal), and they integrate the ability of all pathologists viewing the “webex” like session to download and annotate images in real time.

 

Their device does not have any relationship to the WSI. This is what makes eeDAP different, the ability to relate the wsi with the slide. They cannot pre-determine locations to visit on the microscope or record locations visited on the microscope and link those to a wsi.

 

Their abstract about collecting annotations for AI training is similar to our work, but I feel that without the relationship to the WSI, they will miss the opportunity to train algorithms to work with WSIs, and WSIs are part of our current/new reality and WSI archives are being created at a pretty fast pace.

 

Thank you for sharing. I’ll make sure to look for the authors at PI summit. It’s good to know the landscape of things happening. I’ve been distracted so far this year with wrapping up other projects and I am about to get much more tuned into our collaborative work. I’m excited about that.

 

Brandon

 

From: sirintrs@mskcc.org [mailto:sirintrs@mskcc.org]
Sent: Thursday, March 29, 2018 11:14 AM
To: Gallas, Brandon D. <Brandon.Gallas@fda.hhs.gov>
Subject: RE: PI abstract - novel method for automated data acquisition

 

If you patented some of your components, it might be there are some patent infringements. Not to stir the pot.

 

From: Gallas, Brandon D. [mailto:Brandon.Gallas@fda.hhs.gov]
Sent: Thursday, March 29, 2018 9:38 AM
To: Sirintrapun, Sahussapont J./Pathology
Subject: [EXTERNAL] RE: PI abstract - novel method for automated data acquisition

 

Interesting. It does seem to link the microscope image back to the WSI. I’ll read closely.

 

Thank you,

Brandon

 

From: sirintrs@mskcc.org [mailto:sirintrs@mskcc.org]
Sent: Tuesday, March 27, 2018 3:34 PM
To: Gallas, Brandon D. <Brandon.Gallas@fda.hhs.gov>
Subject: Fwd: PI abstract - novel method for automated data acquisition

 

Hi Brandon, I got this froma vendor at USCAP. This sounds a lot like eeDAP

Sent from my iPhone


Begin forwarded message:

From: Gabe Siegel <gabe@augmentiqs.com>
Date: March 26, 2018 at 9:39:08 PM EDT
To: <fuchst@mskcc.org>, <sirintrs@mskcc.org>, <reuterv@mskcc.org>
Subject: [EXTERNAL] PI abstract - novel method for automated data acquisition

Hi to all,

I wish to bring to your attention a new technology with implications for pathology informatics. Called Augmentiqs, this technology was shown for the first time to clinical pathologists at USCAP, and one the MSKCC pathologists who stopped by our booth believed this could be of interest.

Technology Overview:

Augmentiqs integrates within the existing microscope, transforming it into a connected device. An integrated camera with a field of view equal to the eyepiece captures a live view of the stage, while a digital overlay projected on the optical plane enables use of morphometrics, annotations, image comparison, or any other data - while looking through the eyepiece.

With the ability to communicate directly from the microscope, we perform real-time telepathology, sending images directly to SMS, and saving images to LIS patient files.

Pathology Informatics:

By essentially upgrading the microscope with computer capabilities - while not changing the methodology of the pathologist's routine, Augmentiqs is able to record images and metadata while the pathologists work. When considering the comparison to using WSI for digitizing the data, Augmentiqs captures only the region of interest and piggybacks off the work of live cases, both of which allows Augmentiqs to build pathology databases faster, cheaper and with greater clinical relevance. However, Augmentiqs is further unique in that preset parameters can be set up to score the pathology images and corresponding case and metadata based on time spent looking at a particular region, change of objective, use of annotations, saving to case report etc...

To further emphasize the potential, by integrating within the microscope and offering tools which improve the workflow, Augmentiqs is a technology which pathologists would want to use, making large scale data collection easy with an immediate ROI.

I invite you to read the attached abstract submitted to PI in May. The work was performed by Prof. Edmund Sabo based in Haifa, Israel.

About Us:

We're a young company based in Israel. We envision our technology being used by pathologists to speed up workflow, and by AI developers to build learning sets. We also see our product as a platform upon which to eventually run the algorithms within the workflow. On the latter note, we designed our system to act essentially like a cell phone and "app store", where pathologists can choose to integrate 3rd party pathology software (i.e., Visiopharm analytics, ViewsIQ image stitching etc...).

I hope the information above is relevant to Paige and MSKCC. And if so, I would like to explore the possibility of collaboration.

I also invite you to read the telepathology article published in the Journal of Toxicologic Pathology, and to view the product video.

all the best,

Gabe

Gabe Siegel
CEO
www.augmentiqs.com
Phone: +972 544 380 352



Video Link:https://youtu.be/QkU6cHaB9dU

311

We had a T-con today. The agenda/minutes were as follows:

  • Check in on the progress of the eeDAP study at MSKCC.
  • Discussed a few options for collecting the data faster.
  • Funding opportunities.
  • Pathology Visions

More detailed agenda/minutes are archived in the wiki here, and a link can also be found on the main wiki page.

273

This announcement is archived in the wiki here. The link can also be found on the main wiki page.

Minutes:

  • Brandon summarized the MSKCC visit: Install eeDAP, train key readers, and practice data collection.
  • At first, the registration process seemed too onerous for some participants. After sitting at the system, participants were successful with the registration process and became more comfortable and confident. The MSKCC participants should be applauded for their patience and committment.
  • Registration requires a trained person to complete and does take time (3 min/slide). MSKCC identified two research fellows that will be responsible for registering the slides before each study (microscope mode).
  • There were a few documents created to coordinate the readers and help conduct the study: informed consent form for participating pathologists, a form to collect pathologist information and specify that pathologists task list, a cheat sheet for conducting the study, and a definition of a mitosis for use in the study. These documents can be found here.
  • Yukako shared that the day went very well. She said that the different participants echoed excitement about the technology, as is evidenced by the pathology fellows that are volunteering to be the study administrators (perform the registration process and assist with data collection).
  • The eeDAP system is in a sign-out room where other pathologists in the department are able to see the system. They are asking questions and some are volunteering to participate. We will get more than the 3-5 that we planned for (not counting any CSHL pathologists that will participate).
  • They are meeting this week to reinforce the training and make sure all are ready to begin.
  • We are developing an MTA for the equipment.
  • Once the MTA is in place, we will develop an RCA to govern the data collection. Basic elements are that we will collect and share data, publish and keep each other informed on publication plans, and then put the data in the public domain.
  • Lastly, Brandon discussed that he will update the “context of use” of the eeDAP MDDT to be based on the technical abilities and performance. The update will also have more details on the registration accuracy and the image display. The plan is to circulate something with this group near the end of the month and then engage the FDA on the next steps.
267

Subject: Summary of T-con 12 June 2017

Please check out previous announcements on hardware.

We mainly discussed registration accuracy. I summarized that discussion here.

We also discussed the eeDAP study to start at Memorial Sloan Kettering Cancer Center. Installation of hardware is expected to happen June 20, but there is some paper work that is not quite complete. Both parties are working to make it happen as planned. We will discuss that experience at our next T-con.

The current study plan is as follows: 4 slides, 10 FOV’s per slide, size of FOV is 200 um x 200 um = .04 mm^2. The primary question Brandon had was about the size of the FOV for counting mitoses. The FOV sizes in the plan are about 1/6 the size of a high-powered FOV. Joe (MSKCC) said this should be ok since the pathologists are not expected to decide where to count.

Our next item to deal with is rewriting the eeDAP MDDT. If anyone has anything else to discuss, let Brandon know.

265

Hardware Question: Sharing the question and my response for all to be involved.

The Inspirata team is identifying hardware to build an eeDAP system at their location or at the Moffitt center in Tampa. They don't have a stage and controller matching what FDA has used and documented. They are asking if we could use a Zeiss system with a Marzhauser stage and controller and a B/W (not color) camera or an Evos Auto (no oculars).

Question 1 for everyone else: Is it better for us to try and build identical systems or different systems? I can see benefits in either direction.

My quick response: If we use the same hardware, we can finish the eeDAP MDDT with no new major software development.

 

Alternative option 1 (moderately difficult): I think we could make the Marzhauser stage and controller and a B/W camera work. However, we will need to program new communications to the Marzhauser stage and controller.

Alternative option 2 (difficult): The Evos Auto appears to be very similar to a Sakura VisionTek live digital microscope (a device that the MSKCC team has and has wanted to connect). These devices are not currently supported by eeDAP. If there is a way to communicate to these devices outside of their software, support could be developed. If successful, we could collect data on these kind of devices, which could be compared to evaluations from the digital WSI or the microscope (if a microscope system was also available).

Successfully implementing one or both alternatives would expand our specifications and demonstrate that the software can support other devices. The challenge is that development needs to be done where the equipment is, not remotely. Qi and I can help with any development, but the lead development will come from the owner of the hardware unless you want to bring us the device or come for a visit (brief or extended). Check out the software modules related to stage communications at https://github.com/DIDSR/eeDAP/tree/master/src/stages . We will look into the B/W camera.

Brandon

262

Subject: Hardware Update, I forgot comments about USB devices

It was great seeing everyone at PI. It went so fast. Back to work ...

We have two groups that have successfully run eeDAP in digital mode. I encourage the rest of you to do this too. Please try. Qi and I will help.

Now it is time to run eeDAP in microscope mode, this means putting the hardware together. We have documented the hardware we use and requirements for alternate hardware. That information can be found here,

Please review this documentation. It is critical for the MDDT device description.

Perhaps it would be best if all of us had the same hardware in order to trouble shoot problems. The USB devices are easiest to use and don't require special cables and adapters:

  • Camera: Point Grey Grasshopper3 Color (GS3-U3-50S5C-C)
  • Stage Controller: Prior ProScan III (H31XYZE-US/A)
  • Stage: Prior (H101A/B)

I will be restarting the bi-weekly conversations following a similar schedule as before. Let me know if that schedule doesn't work for you.

Brandon

260

The eeDAP videos are in the minutes from our last meeting (LINK) along with other useful information (questions about installing and running eeDAP). Please review.

I knew I shared the eeDAP videos! I shared the minutes in the invite to today's meeting and posted it to the Wiki main page. I'm not sure why I didn't stumble on them during the T-con.

I'm going to have to be more granular in my communications. I have been trying to consolidate information, but no one wants to stop and read more than a couple sentences. I get it. We are all busy.

You may get more emails, but I hope to make the subject of each more clear ... bite size chunks that you can digest quickly. See you Sunday.

WebEx Info for Meeting at Pathology Informatics, 1:30-5pm, Sunday May 21, 2017

258

You should have just received an email from the WSI working group announcing our agenda for the face-to-face meeting Sunday May 21 at Pathology Informatics. If not, you are not yet a member of that group. Please become a member of that group! Here is the link: https://nciphub.org/groups/wsi_working_group/overview . You can see the agenda regardless if you are a member or not. Go to the link I just wrote, the wsi working group page, and you will find links to the agenda and WebEx info. This information is stored in the blog.

We are meeting tomorrow 10am EST. We can talk about the face-to-face meeting agenda and project issues. Please read the MDDT acceptance letter and think about the next steps for that process. We will organize a meeting with FDA MDDT reviewers on the next steps and should have a plan and specific questions for the agency.

I also posted a couple other resources in the WSI working group blog. Check them out.

 

Brandon

257

You should have just received an email from the WSI working group inviting them to participate in the face-to-face meeting and updating them on our activities. If not, you are not yet a member of that group. Please become a member of that group! Here is the link: https://nciphub.org/groups/wsi_working_group/overview

The minutes from our last meeting have been posted to the wiki. Please review and revise. We have uploaded a bunch of stuff: videos of eeDAP in action, registration accuracy results, and the response from the FDA about the MDDT submission. Check it all out.

I still need a few volunteers to do a short eeDAP study in digital mode: 1-2 hours max. We want to present some data at Pathology Informatics. Please contact me: brandon.gallas@fda.hhs.gov

I will be sending a meeting invite for our last T-con before Pathology Informatics. Please join and help make our face-to-face meeting the best it can be. Have you volunteered to present anything?

254

Subject: Recruiting readers for a quick mitotic counting pilot study

I forgot one more question/announcement. I think it would be fantastic to have some nominal amount of data to present at Pathology Informatics. We have a small a study that we have created as a pilot. We estimate that it will take about 1 hour to execute in digital mode (based on one non-pathologist doing the study). Can anyone recruit a couple readers for this quick and dirty test run?

Brandon

252

Assignments and Agenda for T-con on 5/3, 10am EST. You can also find this item archived in our blog (Link Here)

I am reposting the assignments that I included in the minutes from the last meeting. Please let me know if you have any problems with your assignment.

The meeting agenda will be a discussion of the results from the assignments.

  • Updates from each group on downloading and test driving eeDAP in digital mode.
    • NOBODY tried. This was supposed to be a necessary but not hugely challenging task.
    • Who will be first? I will have a prize of symbolic value. Please let me know if and when you complete this assignment so we can handle this in advance of the T-con.
    • Upddate: Philips and Inspirata appear to have downloaded eeDAP. Inspirata, may have successfully run the program. Tip of the day: the input file must be edited for the the WSI image. At a minimum, you need to specify the filename (keep the full path name short as it can fail otherwise), scanner resolution (from image properties), and the FOV locations (determined from your current WSI viewer). We will provide an input file for an internet-accesible WSI image to ease this first time run. We will update the user manual to note this and that the FOV locations can be chosen with another WSI viewer.
    • Refer to the manual.
  • Update from James Monaco on the Inspirata team protocol (refer to the wiki page for the current version LINK)
    • I am asking that James update his protocol to address more items identified in the STARD checklist (Standards for Reporting Diagnostic Accuracy Studies).
    • I am assigning Philips, CSHL and Darren Treanor to review and provide feedback or questions by email before (and at) our next meeting.
  • Update from Brandon Gallas on the FDA team protocol (refer to the wiki page for the current version LINK).
    • I am asking ITT, MSKCC, and NCI to review this protocol and provide feedback by email before (and at) our next meeting.
    • I am also asking MSKCC and NCI provide a supplement to or otherwise update this protocol to specify the research questions they want to answer (e.g. the devices they want to compare) and the logistics they are arranging for data collection (location and readers they plan to recruit).
  • Discuss registration accuracy: Philips lead? Use a calibration slide.
    • I am asking Philips to outline a protocol for evaluating registration precision. Related, we need to figure out if or how to read the Philips proprietary file format iSyntax and BigTiff with eeDAP. I hope that Philips would work with the open-source community to make their images accessible for the storage and manipulation of biological microscopy data.
    • The FDA team is also setting up a quick registration accuracy evaluation.
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Are you ready for the T-con?

Agenda:

  1. Updates from each group on downloading and test driving eeDAP in digital mode.
  2. Update from James Monaco on the Inspirata team protocol (LINK). Can someone review this ahead of time and have feedback ready for the T-con? CSHL?
  3. Update from Brandon Gallas on the FDA team protocol (LINK). Can someone review this ahead of time and have feedback ready for the T-con? MSKCC?
  4. Discuss registration precision: Philips lead?

 

I will try and archive all announcements in the blog.

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