Microscopy Python Packages

nd2

Full-featured nd2 (Nikon NIS Elements) file reader for python. Outputs to numpy, dask, and xarray. Exhaustive metadata extraction

ngff-zarr

A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.

bioio-base

Typing, base classes, and more for BioIO projects.

bioio

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

cloud-volume

Read and write Neuroglancer datasets programmatically.

cucim

cuCIM - RAPIDS GPU-accelerated image processing library

bioio-tifffile

A BioIO reader plugin for reading TIFFs using Tifffile

bioio-ome-tiff

A BioIO reader plugin for reading Tiff files in the OME format.

cucim-cu12

cuCIM - RAPIDS GPU-accelerated image processing library

bioio-czi

A BioIO reader plugin for reading CZI files.

bioio-nd2

A BioIO reader plugin for reading ND2 images.

ncolor

Fast 4-coloring of instance segmentation label images (N-color relabeling) for Python, C++ core

bioio-lif

A BioIO reader plugin for reading LIF (Leica Image File) images.

bioio-ome-zarr

A BioIO reader plugin for reading Zarr files in the OME format.

brainglobe-atlasapi

A Python interface to access neuroanatomical atlases

nd2reader

Pure Python library for reading NIS Elements ND2 images and metadata

useq-schema

An implementation agnostic schema for describing a sequence of events during a multi-dimensional imaging acquisition.

aicsimageio

Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python

bioio-imageio

A BioIO reader plugin for reading simple image and movie formats

pymmcore-plus

Pure python/C++ micro-manager ecosystem

pycytominer

Python package for image-based profiling

fileglancer

Browse, share, and publish OME-Zarr data

bioio-dv

A BioIO reader plugin for reading Digital Video (DV) files.

cucim-cu13

cuCIM - RAPIDS GPU-accelerated image processing library