k-dominik

ndv

Simple, fast-loading, n-dimensional array viewer with minimal dependencies.

ilastik

ilastik-shell, applets, and workflows to string them together.

naparimovie

Create movies from series of key-frames in napari.

multiscale_read

Read xarray.DataArrays from multiscale datasets with various metadata standards

ImageJ-Fiji_UsefulTools

OsteoclastsWorkflow-Tutorial

Incorporating Machine learning tools into Image Analysis workflows using Fiji, Ilastik and StarDist

torch-em

Deep-learning based semantic and instance segmentation for 3D Electron Microscopy and other bioimage analysis problems based on pytorch.

simde

Implementations of SIMD instruction sets for systems which don't natively support them.

sse2neon

A translator from Intel SSE intrinsics to Arm/Aarch64 NEON implementation

aics-automated-cell-culture-workflow

Venus method files in the “.pkg” format for the Semi Automated Passaging, Seeding and Maintenance, of the Allen cell collection of hiPSC lines expressing green fluorescent protein tagged to protein identifying specific cellular organelles and structures.

spec-bioimage-io

Specification for the bioimage.io model description file.

python-marshmallow-union

Union fields for marshmallow.

tree-sitter-sql

SQL syntax highlighting for tree-sitter

tifffile

Read and write TIFF files

iMMPY

ilastik Mother Machine Python protocol

n5

Not HDF5

conda-tree

conda dependency tree helper

conda-depgraph

A command-line utility to plot the dependency graph of a Conda environment.

cluster_tools

Distributed segmentation for bio-image-analysis

pybind11

Seamless operability between C++11 and Python

pytorch-3dunet

3D U-Net model for volumetric semantic segmentation written in pytorch

napari

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

cpr

C++ Requests: Curl for People, a spiritual port of Python Requests.

cpp_cookiecutter

A cookiecutter template for a modern C++ project with python bindings

neuroglancer

WebGL-based viewer for volumetric data

CppCoreGuidelines

The C++ Core Guidelines are a set of tried-and-true guidelines, rules, and best practices about coding in C++

cloud-volume

Read and write Neuroglancer datasets programmatically.

apistar

The Web API toolkit. 🛠

fastfilters

Old academic project for my PhD - no longer maintained by me: fast gaussian and derivative convolutional filters

awesome-modern-cpp

A collection of resources on modern C++