Jakub Kaczmarzyk
kaczmarj
MD-PhD student interested in medical imaging and computer vision.
Languages
Loading contributions...
Top Repositories
Apptainer in Docker!
[DEPRECATED: use MNE-Python] Python module to stream and analyze EEG data in real-time
Use LabStreamingLayer to handle triggers with PsychoPy.
HIPPO 🦛 is an explainable AI method and toolkit for weakly-supervised models in computational pathology. It enables hypothesis testing on tissue and searching for high-effect and low-effect tissue regions.
Dockerfile to build ANTs from source
Convert GeoJSON of polygons to pyramical TIF images
Repositories
225Use LabStreamingLayer to handle triggers with PsychoPy.
HIPPO 🦛 is an explainable AI method and toolkit for weakly-supervised models in computational pathology. It enables hypothesis testing on tissue and searching for high-effect and low-effect tissue regions.
Data-efficient and weakly supervised computational pathology on whole slide images - Nature Biomedical Engineering
Tool for robust segmentation of >100 important anatomical structures in CT and MR images
Apptainer in Docker!
A platform for end-to-end development of machine learning solutions in biomedical imaging
Backup dropbox directory onto local filesystem
The latex template for Stony Brook University Ph.D. and MS Thesis
🦈 Predicting breast cancer recurrence and intrinsic subtypes with pathology and AI.
This project contains command line tools to perform rigid, affine and non-linear registration of nifti or analyse images as well as utilities
scikit-learn: machine learning in Python
PyTorch code for Vision Transformers training with the Self-Supervised learning method DINO
QuPath documentation
Simple web server to remotely access a raspberrypi controlled automated watering system.
[DEPRECATED: use MNE-Python] Python module to stream and analyze EEG data in real-time
Convert GeoJSON of polygons to pyramical TIF images
Ying's tools for analysis, with particular focus on microbiome data
https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2
TiffSlide - cloud native openslide-python replacement based on tifffile
Deep learning library for digital pathology, with both Tensorflow and PyTorch support.
Segmentation models with pretrained backbones. PyTorch.
First commit
A conda-smithy repository for openslide.
A conda-smithy repository for wsinfer.
QuPath extension to work with WSInfer - https://wsinfer.readthedocs.io/
No description provided.
Dockerfile to build ANTs from source
Deep learning framework to train, deploy, and ship AI products Lightning fast.
DSMIL: Dual-stream multiple instance learning networks for tumor detection in Whole Slide Image
A graph-transformer for whole slide image classification