kaczmarj

apptainer-in-docker

Apptainer in Docker!

lightning

Deep learning framework to train, deploy, and ship AI products Lightning fast.

model-inference-plugin-rdf

Python plugin to write cell segmentation/classification model outputs to RDF file.

NYT-word-of-the-day

Meanings of words from NYT Word of the Day

wsinfer-feedstock

A conda-smithy repository for wsinfer.

23e_urp

Code for the 2023 CSHL URP Python Programming Course

anonymize-survival

CLAM

Data-efficient and weakly supervised computational pathology on whole slide images - Nature Biomedical Engineering

dsmil-wsi

DSMIL: Dual-stream multiple instance learning networks for tumor detection in Whole Slide Image

evoaug

hover_net

Simultaneous Nuclear Instance Segmentation and Classification in H&E Histology Images.

imagecodecs_build

kaczmarj.github.io

Personal site for Jakub Kaczmarzyk

MCAT

Multimodal Co-Attention Transformer for Survival Prediction in Gigapixel Whole Slide Images - ICCV 2021

openslide-feedstock

A conda-smithy repository for openslide.

pcam

The PatchCamelyon (PCam) deep learning classification benchmark.

pyinstaller-docker-linux-windows

Docker image to build PyInstaller apps for broadly compatible Linux and Windows

qupath-docs

QuPath documentation

RetCCL

safetensors

Simple, safe way to store and distribute tensors

scikit-learn

scikit-learn: machine learning in Python

singularity-docker

docker base images to provide release versions of Singularity

slideflow

Deep learning library for digital pathology, with both Tensorflow and PyTorch support.

staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

testing

TESTING-qupath-extension-wsinfer

QuPath extension to work with WSInfer - https://wsinfer.readthedocs.io/

tiffslide

TiffSlide - cloud native openslide-python replacement based on tifffile

til_align

TIL Alignment

tmi2022

A graph-transformer for whole slide image classification

wsinfer-manuscript

Artifacts for the WSInfer manuscript