FynnBe

ilastik

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

05_image_segmentation

collection-bioimage-io

RDF collection for BioImage.IO

tiktorch

Wrappers for Pytorch

torch-em

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

BiaPy-bioimage-io

BiaPy's BMZ connection

bioimage-io-models

Model repository for bioimage.io

bioimage-io-models-1

Model repo for bioimage.io

bioimage.io

Website for the BioImage Model zoo -- a model zoo for bioimage analysis.

bioimageio-ambitious-sloth

draft for a model repo

bioimageio-contribute

common resources for bioimageio contributions

dataclass-argparse

Define command line arguments as type annotated namespace dataclasses

DL-MBL-2021

Exercise repository for the DL@MBL 2021 Course

elf

Utils and convenience functions for large-scale bio-image analysis.

HPA-model-zoo

A collection of deep learning models for analyzing the Human Protein Atlas images.

hypha

A serverless application framework for large-scale data management and AI model serving

inferno

A utility library around PyTorch

models

nucleoli_segment

plant-seg

A tool for cell instance aware segmentation in densely packed 3D volumetric images

processing-bioimage-io-draft

draft pre- and postprocessing with docker images

pydantic

Data validation using Python type hints

pydantic-core

Core validation logic for pydantic written in rust

qupath-bioimage-io

QuPath resources for Bioimage.IO

sandbox

schemastore

A collection of JSON schema files including full API

spec-bioimage-io

Specification for the bioimage.io model description file.

stardist

StarDist - Object Detection with Star-convex Shapes

training-material

A collection of Galaxy-related training material

ZeroCostDL4Mic

ZeroCostDL4Mic: A Google Colab based no-cost toolbox to explore Deep-Learning in Microscopy