Assignments and Agenda for T-con on 5/3, 10am EST
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 IIT, 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.