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05_image_segmentation

augment

Simple elastic augmentation for ND arrays

catmaid

Collaborative Annotation Toolkit for Massive Amounts of Image Data

catmaid-autoproofreader

catmaid-synapsesuggestor

centriole_data

scripts for scraping annotation data from CATMAID and computing some stats

cnnectome.conversion

scripts and helper functions for converting trained tensorflow cnnectome models to pytorch

comatch

Bi-partite matching of nodes to minimize component split/merge errors

contextnet

library and scripts for training models with arbitrarily large context

cookiecutter-rust-pypackage

Cookiecutter template for a Python package.

core-bioimage-io-python

Python libraries for loading, running and packaging bioimage.io models

dacapo

dacapo-dashboard

dacapo-nextflow

Repo for running dacapo via nextflow tower

dacapo-plugins

dacapo plugin example

dacapo_tutorials

some dacapo experiments

daisy

Block-wise task scheduling for large nD volumes.

data-handler

Formalize scripts for gathering data from various sources and pass it to the floodfilling skeletons

deep-channel

To follow

diluvian

Flood filling networks for segmenting electron microscopy of neural tissue

everything-will-be-fine

Semantic Segmentation DL@MBL-2023 team

fibsem-tools

Tools for handling FIB-SEM data and annotations

fragment-skeleton-mapping-scripts

funlib.evaluate

funlib.geometry

A package for Coordinates, Rois and common operations in Coordinate spaces

funlib.learn.tensorflow

Commonly used `tensorflow` models and losses.

funlib.learn.torch

funlib.match

Graph-matching algorithms

funlib.run

funlib.segment

Tools to segment graphs and volumes