Microscopy Images Python Packages

cloud-volume

Read and write Neuroglancer datasets programmatically.

38K 173 53

nd2reader

Pure Python library for reading NIS Elements ND2 images and metadata

7K 49 31

microfilm

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

2K 82 8

laptrack

Particle tracking by solving linear assignment problem.

2K 64 4

particleanalyzer

SEM Image Analysis Tool

2K 18 4

minicontourfinder

Lightweight image segmentation software for biological images

2K 1 0

fibermorph

Interactive toolkit for analyzing hair fiber morphology with GUI and CLI

949 2 3

piscat

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

693 21 14

domb-napari

napari plugin for analyzing fluorescence-labeled proteins redistribution

486 1 0

napari-czitools

Plugin to read CZI image files and their metadata

454 13 1

psf-analysis-cfim

A continuation of napari_psf_analysis, developed for CFIM - KU

337 2 0

tspng

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

269 2 0

cellcyclenet

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

228 10 0

miplib

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

214 89 26

doubleblind

Automatically and reversibly replace file names with random strings to help experimenters quantify microscopy experiments blindly and maintain experimental integrity.

203 0 1

zetastitcher

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

186 47 7

multifocal-stitching

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

159 12 0

fluospotter

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

112 3 0

quoll-compatible-miplib

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

99 89 26

napari-bleach-correct

A napari plugin to correct time-lapse images for photobleaching.

74 4 0

pyimq

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

44 22 8

scellseg

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

33 10 2