Open-source tools for computational pathology: whole slide image (WSI) analysis, deep learning for histopathology, and the QuIP platform for storing, viewing, and sharing results.
Website: bmi.stonybrookmedicine.edu
| Repo | What it is |
|---|---|
| wsinfer | Patch-based classification pipeline for whole slide images. Pretrained models in wsinfer-zoo. |
| champkit | Benchmarking toolkit for patch-based histopathology image classification. |
| SpinPath | CLI for specimen-level inference on whole slide images. |
| quip_distro | Docker Compose distribution of the QuIP platform: caMicroscope viewer, PathDB, and analysis services. |
| PathDB | Image and annotation database behind QuIP. |
| Repo | What it is |
|---|---|
| quip_cnn_segmentation | CNN nucleus segmentation. |
| quip_cancer_segmentation | Tumor region segmentation. |
| quip_classification | Patch classification models. |
| u24_lymphocyte | Tumor-infiltrating lymphocyte (TIL) detection. |
| quip_paad_cancer_detection, quip_prad_cancer_detection, quip_lung_cancer_detection | Cancer-type-specific detection models. |
| histopathology_analysis | Deep learning methods for histopathology image analysis. |
| deep_survival_analysis, tumor-til-survival-analysis | Survival analysis from image features. |
| Repo | What it is |
|---|---|
| cancer-data-bridge | REST API bridging caMicroscope, 3D Slicer, and MongoDB. |
| findapi | Minimal REST interface to MongoDB collections. |
| SegmentationLoader | Load WSI segmentations into MongoDB. |
| featuremap_util | Convert prediction outputs into PathDB featuremaps. |
| manifest_util | Generate upload manifests for PathDB. |
| quip_reports | Export image and annotation inventory reports. |
| quip_converter | Convert vendor slide formats to tiled multiresolution TIFF. |
| Repo | What it is |
|---|---|
| SlicerPathology | 3D Slicer extension for pathology segmentation. |
| nscale | High-performance image analysis libraries (C++, MPI). |
| region-templates | Region Templates runtime for large-scale image analysis. |
| MappingOHDSI2HDF5 | JSON mappings from OHDSI tables to HDF5. |
This work is supported by NCI U24 and related awards. See individual repositories for grant acknowledgements.
Most repositories are released under the BSD 3-Clause License. Check each repository's LICENSE file.
