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1cpn-model

1CPN Coarse-grained model of chromatin

arboretum

Track and lineage visualization with btrack, LapTrack and Napari

automated_lsm

Automation of Zeiss LSM microscopy via macro

basicpy

basicpy-docker-mcmicro

bibverifier

cellpose

a generalist algorithm for cellular segmentation

docker-gpu-conda

Docker image for conda with Cuda and Miniconda

docx-researchmap

exputils

experiment utilities in python

image_analysis_cookbook

Some random python pieces to explain image analysis

ising_simulator

A simple simulator for the Ising model for exhibition / demonstration

laptrack

Particle tracking by solving linear assignment problem.

m2stitch

MIST-inspired microscope image stitching package

micro-manager

Microscope control and image acquisition integrated with ImageJ.

microflow

Nextflow, Jupyter and papermill-based notebooks and workflow for microscopy image preprocessing.

microscopy_image_segmentation

Image segmentation / summarization workflow for zarr images.

microscopy_shadow_correction_stitching

Snakemake workflow for shadow correction and stitching of Zeiss CZI files

microtailor

A tweakable microscopy image stitching library for n-dimensional data

mist

Microscopy Image Stitching Tool

multiview-stitcher

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

napari-amdtrk-plugin

Napari plugin to manually amend live-cell imaging tracks

napari-basicpy

napari-gelanalyzer

Electrophoresis gel analyzer with napari

napari-laptrack

Tracking particles in Napari, using the LapTrack library

napari-segmentation-human-in-loop

Another implementation of human-in-loop segmentation training in napari.

napari-travali

Cell track editor based on napari

nfcore-modules

Repository to host tool-specific module files for the Nextflow DSL2 community!

polus-plugins

pycziutils

A tiny utility module to parse Zeiss CZI files in Python through python-bioformats.