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.

cucim

cuCIM - RAPIDS GPU-accelerated image processing library

bioio

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

ngff-zarr

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

bioio-tifffile

A BioIO reader plugin for reading TIFFs using Tifffile

brainglobe-atlasapi

A Python interface to access neuroanatomical atlases

bioio-ome-tiff

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

cucim-cu12

cuCIM - RAPIDS GPU-accelerated image processing library

atomai

Deep and Machine Learning for Microscopy

pymmcore-plus

Pure python/C++ micro-manager ecosystem

useq-schema

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

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

bioio-nd2

A BioIO reader plugin for reading ND2 images.

nd2reader

Pure Python library for reading NIS Elements ND2 images and metadata

pyclesperanto-prototype

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

cellfinder

Automated 3D cell detection in very large images

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

qpimage

Python library for manipulating quantitative phase images