jni

skan

Python module to analyse skeleton (thin object) images

affinder

Quickly find the affine matrix mapping one image to another using manual correspondence points annotation

napari

Napari PyQt5 and VisPy based GUI plugin

scikit-image

Image Processing SciKit (Toolbox for SciPy)

annotrack

Napari plugin for annotating errors in object trajectories

config

A master repository for all my configuration files

defdap

A python library for correlating EBSD and HRDIC data

HAPPy

A software package to analyse radial hydrides present in light optical and scanning electron micrographs

ilovesymposia.com

Source for ilovesymposia.com

iterseg

napari plugin for iteratively improving 3D instance segmentation of cells (u-net x watershed)

magicgui

build GUIs from python functions, using magic.

matplotlib

matplotlib: plotting with Python

napari-animation

A napari plugin for making animations

napari-defdap

Simple wrapper around DefDAP functionality

napari-docs

Documentation for napari (other than API docs)

napari-graph

Efficient graph data structures and algorithms for fast slicing, visualization, and editing

napari-plugin-template

A template repo used to make new napari plugins

napari-release-tools

Tools for speedup napari release process

napari-sphinx-theme

napari-svg

A plugin for writing svg files from napari

napari-tiff

A napari reader plugin for tiff images.

nd2

Full-featured nd2 (Nikon NIS Elements) file reader for python. Outputs to numpy, dask, and xarray. Exhaustive metadata extraction

ngff

Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.

platelet-analysis-1

A python package for analysing platelet movement

platelet-tracking

A small napari plugin for tracking platelets

pooch

A friend to fetch your data files

scipy-2023-tutorial

tracktour

network-flow based object tracking

useful-histories

My repository for particularly useful analyses carried out in IPython (not the notebook)

vispy

Main repository for Vispy