kate-elfer / eedap

Evaluation Environment for Digital and Analog Pathology

eeDAP

Evaluation Environment for Digital and Analog Pathology

eeDAP is a software and hardware platform for designing and executing digital and analog pathology studies where evaluation regions of interest (ROIs) in the digital image are registered to the real-time view on the microscope. This registration allows for the reduction or elimination of a large source of variability in comparing these modalities in the hands of the pathologist: the field of view (the tissue) being evaluated. In fact, the current registration precision of eeDAP allows for the presentation of the same individual cell in both domains. As such, a study can be designed where pathologists are asked to evaluate a pre-selected list of individual cells in Digital mode and Microscope real-time mode (MicroRT mode). eeDAP collects the pathologist evaluations while cycling through the list of cells. In Digital mode, the pathologist can enter the evaluations himself or herself. In MicroRT mode, an administrator enters the evaluations while confirming and maintaining a high level of registration precision. The paired observations allow for comparisons of WSI and traditional optical microscopy using several forms of agreement or performance when a reference standard can be established.

Related references (please cite)

Gallas, Brandon D., Marios A. Gavrielides, Catherine Conway, Adam Ivansky, Tyler Keay, Wei-Chung Cheng, Jason Hipp, and Stephen M. Hewitt. “Evaluation Environment for Digital and Analog Pathology (EeDAP): A Platform for Validation Studies.” J Med Img 1 (2014): 037501. https://doi.org/10.1117/1.JMI.1.3.037501.

Q. Gong, B. P. Berman, M. A. Gavrielides, and B. D. Gallas, “Registration accuracy between whole slide images and glass slides in eeDAP workflow,” in Medical imaging 2018: digital pathology, 2018, vol. 10581. https://doi.org/10.1117/12.2293189

User Manual

Click to go to the user manual.
Here are demo videos for running eeDAP in digital mode and microRT mode.

Releases = Packages

Click to go to the releases page.
Click to go to a description of release updates.

We hope you are interested in trying our software. Please know that we are willing to help you in many ways: set-up of hardware, modifying the tasks for your application, and even the design and execution of your study. Of course, help with the design and execution of a study depends on our capacity and alignment with our mission.

Similarly we hope you will provide feedback on the software and documentation so that we can make this project the best it can be.

Please check out a statement of the licenses related to our software here.

Related Resources and References

Click to go to the list of resources and references.

This list includes appropriate means by which you can reference our work.

eedap's Issues

Ludl stage COM port

Running eeDAP with MATLAB R2022a

@kate-elfer @k-blenman
Hi all,

Less of an issue and more of an update -- I have eeDAP up and running in Digital Mode on my Windows laptop. Here are some of the obstacles I faced before I could do so:

• It was clear from the manual that I needed to use MATLAB Runtime R2016a (Version 9.0.1) in order for eeDAP to run. At the time I had the most recent version of MATLAB installed (R2022a). I kept on getting a similar error to the following: https://www.mathworks.com/matlabcentral/answers/93249-why-does-the-matlab-installer-quit-after-configuring-microsoft-visual-c-redistributable#:~:text=This%20behavior%20indicates%20that%20the,you%20can%20complete%20the%20installation.&text=Most%20of%20the%20time%2C%20rebooting,which%20can%20fix%20the%20issue. Every time I tried downloading and updating Runtime, the MATLAB installer quit while configuring the Microsoft Visual C++ Redistributable.
• While downloading eeDAP without Admin privileges (.zip file): at this point I hadn't found the link above yet to solve my issue, so I downloaded MATLAB R2016a with its corresponding update, then had no issues installing the appropriate Runtime version after that and thus running eeDAP per the manual instructions. Once I followed the instructions from the link above to install the Microsoft Visual C++ Redistributable manually and rebooted my computer, I was also able to run eeDAP in the most current MATLAB version -- this was an issue on my end.
• Running eeDAP with Admin privileges (.exe file): once I had done the above, I had no issues running eeDAP directly from the .exe file, as per the manual instructions.

Some edits for the manual:

• In the DIDSR/eeDAP user manual, it is mentioned that the MCR version required for Windows is R2016a (9.1.1) -- should be 9.0.1, but this small error was negligible and I could figure it out. Just for future versions of the manual! :)
• In Kate's version of the manual, I could not find any mention of the specific MCR version required, just that the user needs to have the same version used for the original eeDAP code ("The MCR library must be the same version as was used to create the stand-alone application."). Could be that I missed this mentioned somewhere else -- once I downloaded eeDAP without admin privileges (the zip file version), this requirement was spelled out in that folder's README file. I'm sure your changes will be merged with the main eeDAP page, but I think it would be helpful to mention the specific version requirement several times throughout the updated manual, especially under the section "Download and Install", and again under Software Requirements like originally done. Redundancy would be helpful :)
• Under "Matlab Compiler Runtime Libraries", the link for the Medviso MCR installer does not work anymore.

Thanks!

Victoria