Microscopy Images Python Packages

cloud-volume

Read and write Neuroglancer datasets programmatically.

nd2reader

Pure Python library for reading NIS Elements ND2 images and metadata

micro-sam

Segment Anything for Microscopy

python-elf

Utility functions for large-scale bio-image analysis.

laptrack

Particle tracking by solving linear assignment problem.

microfilm

Creating figures and animations for multi-channel images with a focus on microscopy.

particleanalyzer

SEM Image Analysis Tool

minicontourfinder

Lightweight image segmentation software for biological images

fibermorph

Image analysis tool to measure hair cross-sectional micrographs and hair curvature images.

domb-napari

napari plugin for analyzing fluorescence-labeled proteins redistribution

piscat

PiSCAT is a python-based package with a graphical user interface for performing high-performance analysis on a variety of iSCAT measurements.

napari-czitools

napari plugin to open CZI image files and their metadata

psf-analysis-cfim

A continuation of napari-psf-analysis for CFIM

miplib

A Python software library for (optical) microscopy image restoration, reconstruction and analysis.

cellcyclenet

Predicting cell cycle stage from 3D single-cell nuclear-stained images

zetastitcher

ZetaStitcher is a tool designed to stitch large volumetric images such as those produced by Light-Sheet Fluorescence Microscopes.

doubleblind

Blind and unblind file names automatically to maintain experimental integrity

tspng

A Python package for manipulating PNG files with embedded JSON related to Machine Learning.

multifocal-stitching

Python package for microscope image stitching, robust to image pairs taken at different focal lengths and translations

fluospotter

Python library designed for nuclei segmentation and puncta detection in fluorescence microscopy images.

quoll-compatible-miplib

A Python software library with a variety of functions for (optical) microscopy image restoration, reconstruction and analysis.

napari-bleach-correct

Napari Photobleach Correction

scellseg

A style-aware deep learning model for adaptive cell instance segmentation by contrastive fine-tuning.

pyimq

A Python library for easily calculating image-quality related features from images