Microscopy Python Packages

aicsimageio

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

cloud-volume

Read and write Neuroglancer datasets programmatically.

nd2

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

bioio-base

Typing, base classes, and more for BioIO projects.

ngff-zarr

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

cucim

cuCIM - RAPIDS GPU-accelerated image processing library

bioio

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

pymmcore-plus

Pure python/C++ micro-manager ecosystem

cucim-cu12

cuCIM - RAPIDS GPU-accelerated image processing library

bioio-tifffile

A BioIO reader plugin for reading TIFFs using Tifffile

useq-schema

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

brainglobe-atlasapi

A Python interface to access neuroanatomical atlases

bioio-ome-tiff

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

bioio-czi

A BioIO reader plugin for reading CZI files.

bioio-ome-zarr

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

bioio-imageio

A BioIO reader plugin for reading simple image and movie formats

pyclesperanto-prototype

GPU-accelerated bio-image analysis focusing on 3D+t microscopy image data

nd2reader

Pure Python library for reading NIS Elements ND2 images and metadata

bioio-nd2

A BioIO reader plugin for reading ND2 images.

cellfinder

Automated 3D cell detection in very large images

fileglancer

Browse, share, and publish OME-Zarr data

bioio-lif

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

nanomesh

Python workflow tool for generating meshes from 2D and 3D image data

cp-measure

Morphological features from images and masks made easy.