NHPatterson

segment-anything

The repository provides code for running inference with the SegmentAnything Model (SAM), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.

pydantic-ome-ngff

Pydantic models for OME-NGFF

timsconvert

tiffslide

TiffSlide - cloud native openslide-python replacement based on tifffile

bioio

Image reading, metadata management, and image writing for Microscopy images in Python

mmv_im2im

Python package for deep learning based image to image transformation

JaneliaMLCourse

pizzarr

Slice into Zarr arrays in R 🍕

memray

Memray is a memory profiler for Python

napari-graph

Efficient graph data structures and algorithms for fast slicing, visualization, and editing

ngff

Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.

napari-workflow-inspector

Inspect relationships between napari-plugins in active workflows.

napari-imsmicrolink

napari plugin for IMS - Microscopy registration through laser ablation marks.

ngff-writer

A writer and reader for NGFF OME-Zarr datasets

asms-2021-r-shortcourse

Materials for the ASMS 2021 Getting Started with R Short Course

MSIandCo

Mass spectrometry imaging and complementary techniques open collaboration

tifffile

Read and write TIFF files

bfio

Interface to the Bioformats Java library

napari-plot

1d plotting in napari-based canvas.

MSIWarp

MAss spectra alignment tool for MSI data

SimpleITK

SimpleITK: a layer built on top of the Insight Toolkit (ITK), intended to simplify and facilitate ITK's use in rapid prototyping, education and interpreted languages.

ITKElastix

An ITK Python interface to elastix, a toolbox for rigid and nonrigid registration of images

napari

napari: a fast, interactive, multi-dimensional image viewer for python

SimpleElastix

Multi-lingual medical image registration library