Jason L Weirather's repositories
hla-polysolver
Fork of the Polysolver project
pythologist
Read and analyze exports of microscopy image data.
good-neighbors
Identify neighborhoods based on local cell populations.
multiplex-if-simulator
Simulate multiplex IF data
cio-wdl-16s-microbiome
A workflow for executing a microbiome workflow
tiff-inspector
A package for examining the structure and contents of the metadata contained within tiff files
pythologist-reader
Reading functions to generate projects for storage and producing dataframes suitable for pythologist analysis
ark-analysis
Integrated pipeline for multiplexed image analysis
azure-vault-loader
A tool for loading secrets from azure key vault secrets onto remote machines holding proper credentials.
bioformats2raw
Bio-Formats image file format to raw format converter
deepcell-tf
Deep Learning Library for Single Cell Analysis
gonk-diffusers-api
Python API for transforming text into vivid images using Stable Diffusion, with GPU support and concurrency control.
jason-weirather.github.io
Make a cool portfolio repo
kiosk-imageJ-plugin
An ImageJ Plugin for interacting with the DeepCell Kiosk
mantis-viewer
Electron-based multiplexed imaging viewer
mibitracker-client
Python client for IONpath MIBItracker API, plus utility functions for working with MIBItiff images.
multiplex-imaging-schemas
A library proposing standards for harmonized acquisition of multiplex imaging commonly used in immuno-profiling.
ome-model
OME model (specification, code generator, implementation)
ome-schema
A fork of the Open Microscopy Environment (OME) schema
promptfoo
Test your prompts. Evaluate and compare LLM outputs, catch regressions, and improve prompt quality.
pythologist-image-utilities
Functions for working with image data in python
pythologist-schemas
Check assumptions for input types prior to ingestion.
raw2ometiff
Raw format to OME-TIFF converter
zarr-python
An implementation of chunked, compressed, N-dimensional arrays for Python.