Request for Data Preparation Scripts

[wlin-at]

Dear Authors,

Thank you for your great work. I wanted to ask whether you plan to release the scripts for WSI data preparation (segmentation, patching, and feature extraction). I have been trying to follow the data processing pipelines provided in the CLAM repo, but I encountered a few dataset-specific issues:

Segmentation and filtering hyperparameters.
It seems that the optimal hyperparameters can vary across datasets. For example, the CLAM repo provides presets for TCGA, BWH_biopsy, and BWH_resection, but not for others. I noticed that using unsuitable hyperparameters sometimes leads to stalled feature extraction jobs and zombie processes without raising explicit errors.

Thank you very much for your time and consideration.

Best,

Wei

[wlin-at]

I think I figured out the reason of the feature extraction job stalling. The Dataloader num_workers is harded as 8 in the script.
PyTorch DataLoader with multiple workers (num_workers > 0) is notorious for stalling silently, especially when the dataset (Whole_Slide_Bag_FP) uses libraries like OpenSlide and h5py that aren’t fully multiprocessing-safe. The worker processes get stuck waiting on locks (e.g., HDF5 file handles).

[wlin-at]

When processing WSI datasets (e.g., BRACS), I noticed that the default segmentation and filter parameters sometimes result in zero valid tissue contours being detected. In these cases, the function WSI_object.process_contours(**kwargs) does not generate an .h5 patch file for the corresponding slide.

This leads to situations where:

• A mask .jpg file is still created (from WSI_object.visWSI()),
• But no .h5 file is saved in the patches folder,
• Consequently, no stitch .jpg file is produced either (since stitching requires the .h5 file).

Could you share the hyperparameters used for segmentation and patching for these WSI datasets?

Thanks in advance!