Ryan Carelli

[QST] UMAP Inference (without Python)

1

From the documentation, I could only find support for pickling the UMAP model. I would like to export to a format that supports (GPU) inference without Python. Something like Onnx...

When possible we should read image metadata and save channel names, RGB from openslide or molecule name from bioformats

CAMELYON Datasets

2

Datamodule and Dataloader for https://camelyon17.grand-challenge.org/

Integrate with Viewer

5

The multiplexed MIF workflow requires actively moving back and forth between raw image and phenotype plots to choose optimal phenotype thresholds and check that phenotypes match the pathologist's expectations. At...

Finalize PESO prostate epithelium/stroma segmentation dataset https://www.wouterbulten.nl/blog/tech/peso-dataset-whole-slide-image-prosate-cancer/#:~:text=The%20PESO%20dataset%20consists%20102,total%20dataset%20is%20around%20140GB.&text=62%20whole%2Dslide%20images%2C%20exported,of%20the%20color%20deconvolution%20operation.

When we reshape or get unprocessed data from slide scanners, there may be stitching artifacts that must be detected and removed. - [ ] Choose stitching artifact removal algorithm -...

Add support for tile-level 1. fold detection 2. out of focus detection