Projects in Awesome Lists by kaczmarj
A curated list of projects in awesome lists by kaczmarj .
https://github.com/kaczmarj/apptainer-in-docker
Apptainer in Docker!
apptainer containers docker hpc singularity singularity-container
Last synced: 13 Apr 2025
https://github.com/kaczmarj/rteeg
[DEPRECATED: use MNE-Python] Python module to stream and analyze EEG data in real-time
eeg labstreaminglayer mne-python real-time
Last synced: 30 Apr 2025
https://github.com/kaczmarj/psychopy-lsl
Use LabStreamingLayer to handle triggers with PsychoPy.
eeg labstreaminglayer psychopy python research
Last synced: 06 May 2025
https://github.com/kaczmarj/hippo
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.
Last synced: 26 Mar 2025
https://github.com/kaczmarj/ants-builds
Dockerfile to build ANTs from source
ants docker medical-imaging neuroimaging registration
Last synced: 17 Mar 2025
https://github.com/kaczmarj/geojson2tif
Convert GeoJSON of polygons to pyramical TIF images
image-segmentation machine-learning tiff whole-slide-imaging
Last synced: 26 Mar 2025
https://github.com/kaczmarj/minimal-setup.py-project
Minimal setup.py project that meows at you.
Last synced: 04 Apr 2025
https://github.com/kaczmarj/eeg-analysis
EEG analysis with open-source software (MNE)
Last synced: 04 Apr 2025
https://github.com/kaczmarj/reproenv
Generic Dockerfile and Singularity recipe generator
Last synced: 04 Apr 2025
https://github.com/kaczmarj/hovernet-convert-tf-ckpt-to-npz
Convert HoVerNet TensorFlow checkpoints to NumPy npz format.
Last synced: 04 Apr 2025
https://github.com/kaczmarj/nifti-ts
NIfTI I/O routines implemented in Typescript [experimental]
Last synced: 04 Apr 2025
https://github.com/kaczmarj/meningioma
Segmentation of meningiomas in structural MR images
Last synced: 04 Apr 2025
https://github.com/kaczmarj/model-inference-plugin-rdf
Python plugin to write cell segmentation/classification model outputs to RDF file.
Last synced: 04 Apr 2025
https://github.com/kaczmarj/nyt-word-of-the-day
Meanings of words from NYT Word of the Day
Last synced: 04 Apr 2025
https://github.com/kaczmarj/rtsz-scripts
Scripts for real-time schizophrenia project
Last synced: 04 Apr 2025
https://github.com/kaczmarj/covid19vis
Interactive world map of COVID-19 cases over time
coronavirus covid-19 visualization
Last synced: 04 Apr 2025
https://github.com/kaczmarj/litte_anns
small scale simple artificial neural networks
Last synced: 04 Apr 2025
https://github.com/kaczmarj/classification-of-gbm-vs-pcnsl-using-cnns
Classification of Glioblastoma versus Primary Central Nervous System Lymphoma using Convolutional Neural Networks
Last synced: 04 Apr 2025
https://github.com/kaczmarj/histology-patch-pytorch
Loading histology image patches with pytorch data methods
Last synced: 04 Apr 2025
https://github.com/kaczmarj/convert-hovernet-to-quip
Convert HoVerNet outputs to quip-compatible format
Last synced: 04 Apr 2025
https://github.com/kaczmarj/tumor-microenvironment-analysis
Code related to the analysis of tumor microenvironment in digital whole slide images.
Last synced: 02 Apr 2025
https://github.com/kaczmarj/car-safety-shiny
An R Shiny app -- final project for BMI 530
cars data-visualization nhtsa shiny visualization
Last synced: 02 Apr 2025
https://github.com/kaczmarj/summer-2017-code-prep
Coding prep for summer 2017
Last synced: 04 Apr 2025
https://github.com/kaczmarj/wsinfer-manuscript
Artifacts for the WSInfer manuscript
Last synced: 04 Apr 2025
https://github.com/kaczmarj/rotation-koo-lab
Artifacts from rotation in Koo Lab at CSHL
Last synced: 04 Apr 2025
https://github.com/kaczmarj/nobrainer-js
Predict using trained TensorFlow models in the browser (UNSTABLE)
Last synced: 04 Apr 2025
https://github.com/kaczmarj/docker-golang-example
Example of how to use Docker image on OpenMind
Last synced: 04 Apr 2025
https://github.com/kaczmarj/mindbodylearning
Analysis for the MindBodyLearning study
Last synced: 04 Apr 2025
https://github.com/kaczmarj/histology-bootcamp
Figuring out how to work with histology images. Don't use this code, it's covered in ants.
Last synced: 04 Apr 2025
https://github.com/kaczmarj/diffusion-containers
example of neuroimaging containers for diffusion (and other things)
Last synced: 04 Apr 2025
https://github.com/kaczmarj/git-github-tutorial
Tutorial about git and GitHub aimed at scientists but for anyone
Last synced: 04 Apr 2025
https://github.com/kaczmarj/emr-sample
toy emr server (practice with golang)
Last synced: 04 Apr 2025
https://github.com/kaczmarj/container-examples
Examples of Dockerfiles and Singularity recipes
Last synced: 04 Apr 2025
https://github.com/kaczmarj/mrtrix3-builds
Dockerfile to build MRtrix3 from source
Last synced: 04 Apr 2025
https://github.com/kaczmarj/dbx-backup
Backup dropbox directory onto local filesystem
Last synced: 04 Apr 2025
https://github.com/kaczmarj/test-ppc64le-dockerhub
Test of DockerHub automated builds of ppc64le images
Last synced: 04 Apr 2025
https://github.com/kaczmarj/paad-cell-classifier
command-line interface to classify images of pancreatic cells
Last synced: 04 Apr 2025
https://github.com/kaczmarj/trace-files
WIP: list all of the files used by a process and its offspring
Last synced: 04 Apr 2025
https://github.com/kaczmarj/quip-dots-to-cell-classification-data
Convert dotting labels on QuIP to training data for cell classification.
Last synced: 04 Apr 2025
https://github.com/kaczmarj/mycal
Modify mandatory Stony Brook Medical School events in iCalendar
Last synced: 04 Apr 2025