Microscopy Python Packages

aicsimageio

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

cucim

cuCIM - RAPIDS GPU-accelerated image processing library

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.

bioio

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

nd2

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

cloud-volume

Read and write Neuroglancer datasets programmatically.

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.

sofima

Scalable Optical Flow-based Image Montaging and Alignment

bioio-czi

A BioIO reader plugin for reading CZI files.

useq-schema

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

cucim-cu12

cuCIM - RAPIDS GPU-accelerated image processing library

bioio-ome-zarr

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

brainglobe-atlasapi

A Python interface to access neuroanatomical atlases

pyclesperanto-prototype

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

bioio-imageio

A BioIO reader plugin for reading simple image and movie formats

bioio-nd2

A BioIO reader plugin for reading ND2 images.

pymmcore-plus

Pure python/C++ micro-manager ecosystem

bioio-lif

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

nrefocus

python library for numerical focusing (refocusing, autofocusing) of complex wave fields

qpimage

Python library for manipulating quantitative phase images

nd2reader

Pure Python library for reading NIS Elements ND2 images and metadata

bioio-bioformats

A BioIO reader plugin for reading bioformats formatted images.