The following is a conversation help an eeDAP launch ImageScope. Start at the bottom.
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Hello Keerthi,
Thank you for trying our eeDAP software. I attach a sample input file for CUM-1.ndpi WSI image, which can be downloaded from http://openslide.cs.cmu.edu/download/openslide-testdata/Hamamatsu/CMU-1.ndpi. You should edit this line in the input file “wsi_slot_1 = C:\000_whole_slides\CMU-1.ndpi” to the CMU-1.ndpi saving path.
The bottom part of input file is about kind and ROI for each task. If you want to create an input file for your own image, you should edit them following our manual: http://didsr.github.io/eeDAP/000_EEDAP/manualHTML/input_file_body__list_of_rois_and_corresponding_tasks.htm?ms=AAA%3D&st=MA%3D%3D&sct=MzI%3D&mw=MjQw. For task names, I already set them to “count_imagescope”. For now, we only have this task, which can communicate with ImageScope.
Please update your cloned source code and run the software by source code. Our compiled version eeDAP4p0.exe can’t communicate with ImageScope. Please let us know if you have any other questions. Thank you.
Regards, Qi
On Wed, Apr 26, 2017 at 12:32 PM, Gallas, Brandon D. wrote:
I have added Qi to this email.
You are making progress. We are making notes as to how to improve the user manual. Thanks for your feedback.
We have updated the sample input files to correspond to a WSI image that is available on the web (links to wsi images are inside the input files). Please update what you have from GitHub.
Qi, please help Keerthi to incorporate ImageScope. Maybe create another sample input file with a couple tasks that use “ImageScope”. We will need to address this in the user manual. It is a fairly new feature.
We also need to provide some documentation on selecting fields of view. This has come up a few times now.
Brandon
From: Keerthi Ram
Sent: Tuesday, April 25, 2017 11:09 PM To: Gallas, Brandon D. Subject: Re: eeDAP studies Group Announcement
Dear Brandon,
I am Keerthi from the IIT Madras team, and I would need some help to get the eeDAP software running at our end in virtual mode.
I had actually cloned the github eeDAP repository even prior to our first call early this month. In the first call you had mentioned that eeDAP tool works with ImageScope. I was intending to follow some of the examples given along with the tool.
The specific digital slides (.ndpi files) that the tool looks for by default (e.g. c:\000_whole_slides\100113_Thorlabs_20x.ndpi) were not available on github, and google showed an ftp link that doesn’t seem to be working.
At this point when I point the software to another existing .svs file on my disk (data from The Cancer Genome Atlas) the tool loads with the welcome screen, etc, but I am not sure how to connect it with ImageScope at this point, and the ROIs that are loaded are not relevant.
I have the source code, and I find that the first window that loads is the “Administrator_input_screen.m” .
I looked through the github VI.Workflow pages, but don’t seem to find how to get going with ImageScope as a virtual microscope.
Would you or Qi Gong have quick pointers to get me past this stage and interplay with ImageScope? – keerthi
IIT Madras