wangliyuan72

tqdm

:zap: A Fast, Extensible Progress Bar for Python and CLI

czitools

This repository provides a collection of tools to simplify reading CZI (Carl Zeiss Image) pixel and metadata in Python. In addition it also contains other useful utilities to visualize CZI images inside Napari.

multiview-stitcher

A toolbox for registering / fusing / stitching large multi-view / multi-positioning image datasets in 2-3D.

halfway-to-i2k-skimage-napari

Repo for halfway to i2k workshop: Fundamentals of image analysis in Python with scikit-image, napari, and friends

scientific-python-lectures

Lectures on scientific computing with python, as IPython notebooks.

Mitochondria-Analyzer

Mitochondria Analyzer

SIMPLI

SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.

nellie

Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy

pyclesperanto_prototype

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

Q-VAT

Quantitative Vascular Analysis Tool

SNT

The ImageJ framework for quantification of neuronal anatomy

ijp-imagetoatlas

2D sections to 3D atlas registration with Fiji and QuPath

FASTMAP

ImageJ Plugin for Flexible Atlas Segmentation Tool for Multi-Area Processing

wsinfer

🔥 🚀 Blazingly fast pipeline for patch-based classification in whole slide images

qupath-extension-sam

QuPath extension for Segment Anything Model (SAM)

qupath

QuPath - Bioimage analysis & digital pathology

MuscleJ2

MuscleJ2: a rebuilding of MuscleJ with new features for high-content analysis of skeletal muscle immunofluorescence slides

pyimagej

Use ImageJ from Python

biom3d

Easy Volumetric Segmentation with Deep Learning

pycytominer

Python package for processing image-based profiling data

piximi

deconvolution-gpu-dl-course

Course: Exploring the Intersection of Deconvolution, GPU Computing, and Deep Learning

miniforge

A conda-forge distribution.

bioengine

napari-training-course

Lectures for a napari training course

patchify.py

A library that helps you split image into small, overlappable patches, and merge patches into original image.

PHANTAST-FIJI

Repository for the FIJI/ImageJ implementation of the phase contrast microscopy segmentation toolbox (PHANTAST)

Cell_ACDC

A Python GUI-based framework for segmentation, tracking and cell cycle annotations of microscopy data

QuickFigures

QuickFigures is a toolset for creating scientific figures see publication for details

cellpose-napari

napari plugin for cellpose (see www.cellpose.org) - an anatomical segmentation tool