The Python programming language

Deep Learning for humans

Image Polygonal Annotation with Python (polygon, rectangle, circle, line, point and image-level flag annotation).

SciPy library main repository

napari: a fast, interactive, multi-dimensional image viewer for python

Jupyter Notebook Conversion

The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on d…

StarDist - Object Detection with Star-convex Shapes

build GUIs from type annotations

Bayesian multi-object tracking

starfish: unified pipelines for image-based transcriptomics

The python-microscopy environment - an open-source package for light microscopy

Deep Learning-Based Point-Scanning Super-Resolution (PSSR)

A napari plugin for making animations

Cookiecutter for napari plugins

Accelerated Pixel and Object Classifiers (APOC)

Track and lineage visualization with btrack and Napari 🌲

A minimal YOLO V1 implementation using Keras

StarDist plugin for napari

Segmentation method able to detect membrane/nuclei-labelled cells with low signal-to-noise ratio and dense packing in 2D and 3D. Available via pip package vollseg.

Automatic segmentation of electron microscopy volumes

Tool for segmentation in bioimaging

Open-source, GPU accelerated code for deskewing and deconvolving lattice light sheet data

Python generator for voxel data augmentation

3D shape analysis using deep learning

A plugin to visualise 3D spatial single cell omics

Image deconvolution algorithms in python

A utility to be able to launch jobs on JZ with reasonable defaults

Optimize image processing workflows in napari