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stardist
stardist

StarDist - Object Detection with Star-convex Shapes

34K 1K 271
bioimage-io
bioimageio-core

Python libraries for loading, running and packaging bioimage.io models

22K 35 21
4DNucleome
partseg

Tool for segmentation in bioimaging

17K 37 10
clEsperanto
pyclesperanto-prototype

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

8K 243 49
ScalableCytometryImageProcessing
scip

Scalable Cytometry Image Processing (SCIP) is an open-source tool that implements an image processing pipeline on top of Dask, a distributed computing framework written in Python. SCIP performs projection, illumination correction, image segmentation and masking, and feature extraction.

3K 7 0
danihae
bio-image-unet

Implementation of U-Net, U-Net++, and 3D U-Net in PyTorch for analysis of bio-images

2K 6 1
matjesg
deepflash2

A deep-learning pipeline for segmentation of ambiguous microscopic images.

1K 65 11
jhnnsrs
faser

A python based toolkit for psf estimation using a vectorial model of the electromagnetic field

969 5 0
danihae
sarc-asm

A Python package for AI-based comprehensive analysis of sarcomere structure and function in cardiomyocytes

958 14 3
cytomine
cytomine-python-client

A web platform for collaborative analysis of very large bio-medical images

836 15 5
sanderslab
magellanmapper

MagellanMapper is a graphical interface for 3D bioimage annotation, atlas registration, and regional quantification

265 22 4
MontpellierRessourcesImagerie
napari-j

A plugin to exchange data with FIJI and to use FIJI image analysis from napari

218 2 2
clEsperanto
clesperanto

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

196 243 49
neurobiology-ut
napari-philow

Python-based Human-In-the-LOop Workflow: PHILOW is an interactive deep learning-based platform for 3D datasets

153 26 4
kreshuklab
run-stardist

Train and use StarDist models

138 23 3
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