Microscopy Images Python Packages

cloud-volume

Read and write Neuroglancer datasets programmatically.

28K 176 54

laptrack

Particle tracking by solving linear assignment problem.

13K 69 4

nd2reader

Pure Python library for reading NIS Elements ND2 images and metadata

10K 49 32

python-elf

Utility functions for large-scale bio-image analysis.

3K 64 22

micro-sam

Segment Anything for Microscopy

2K 735 113

particleanalyzer

A Computer Vision-Based Tool for Automatic Segmentation and Size Analysis of Nanoparticles in Scanning Electron Microscope (SEM) and Transmission Electron Microscope (TEM) Images

1K 38 6

tspng

A Python package for manipulating PNG files exported or imported using the Theiascope web application

961 2 0

minicontourfinder

Lightweight image segmentation software for biological images.

933 1 0

microfilm

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

746 83 10

domb-napari

napari plugin for analyzing fluorescence-labeled proteins redistribution

651 1 0

piscat

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

646 21 13

fibermorph

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

631 2 4

napari-czitools

napari plugin to open CZI image files and their metadata

533 17 1

psf-analysis-cfim

A continuation of napari-psf-analysis for CFIM

329 2 0

cellcyclenet

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

163 11 0

doubleblind

Blind and unblind file names automatically to maintain experimental integrity

137 0 1

multifocal-stitching

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

130 14 0

miplib

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

129 90 27

zetastitcher

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

122 46 7

fluospotter

Fluospotter is an end-to-end pipeline designed for nuclei segmentation and puncta detection in fluorescence microscopy images.

82 3 0

quoll-compatible-miplib

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

57 90 27

napari-bleach-correct

Napari Photobleach Correction

50 4 0

scellseg

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

46 10 2

pyimq

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

32 22 8