search

jlevy44 / PathFlowAI

A High-Throughput Workflow for Preprocessing, Deep Learning Analytics and Interpretation in Digital Pathology
https://jlevy44.github.io/PathFlowAI/
MIT License
39 stars 8 forks source link

Testing example #19

Open asmagen opened 4 years ago

asmagen commented 4 years ago

Is there a small example dataset on which I can test if my environment is set up correctly? Also, I get nonechucks may not work properly with this version of PyTorch (1.5.0). It has only been tested on PyTorch versions 1.0, 1.1, and 1.2 when running the preprocess command. Is this a big issue?

jlevy44 commented 4 years ago

Hi @asmagen , the nonechucks warning is not a big issue. Sure, I would recommending pulling data from TCGA. Here is a nice tutorial: http://www.andrewjanowczyk.com/download-tcga-digital-pathology-images-ffpe/ @sumanthratna and I are also in the middle of a PR to add a test pipeline to pathflow, but does contain TCGA data. @sumanthratna has done a really nice job of compiling test data of all forms for the pipeline, here: https://github.com/sumanthratna/PathFlowAI/tree/master/tests/inputs , which will be merged into our main pipeline soon.