Microscopy Images Python Packages

cloud-volume

Read and write Neuroglancer datasets programmatically.

nd2reader

Pure Python library for reading NIS Elements ND2 images and metadata

microfilm

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

laptrack

LapTrack

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

minicontourfinder

Lightweight image segmentation software for biological images.

piscat

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

fibermorph

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

napari-czitools

napari plugin to open CZI image files and their metadata

psf-analysis-cfim

A continuation of napari-psf-analysis for CFIM

domb-napari

napari plugin for analyzing the redistribution of fluorescence-labeled proteins

miplib

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

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

cellcyclenet

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

multifocal-stitching

Algorithms and tools for stitching microscopy images taken at different focal lengths

fluospotter

Fluospotter is an end-to-end pipeline 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