pattonw

CATMAID-autoproofreader

neurolight

05_image_segmentation

CATMAID

Collaborative Annotation Toolkit for Massive Amounts of Image Data

centriole_data

scripts for scraping annotation data from CATMAID and computing some stats

comatch

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

cookiecutter-rust-pypackage

Cookiecutter template for a Python package.

dacapo-dashboard

dacapo-nextflow

Repo for running dacapo via nextflow tower

dacapo-plugins

dacapo plugin example

dacapo_tutorials

some dacapo experiments

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

fragment-skeleton-mapping-scripts

funlib.evaluate

funlib.learn.tensorflow

Commonly used `tensorflow` models and losses.

funlib.match

Graph-matching algorithms

funlib.run

funlib.segment

Tools to segment graphs and volumes

funlib_match_helpers

helper functions for funlib match to speed up ILP initialization

i2k_gunpowder_tutorial

Gunpowder tutorial given at the I2K 2020 conference

maximin

Calculate the maximin path between any set of points from a 3d numpy array of intensities

micron

mouselight

ML experiments on mouse light microscopy data

neuroglancer_graphs

some helpful scripts for visuallizing graphs in neuroglancer

neurolight_evaluation

Evaluation methods for sparse neuron segmentation

pyo3-pack

Build and publish crates with pyo3, rust-cpython and cffi bindings as well as rust binaries as python packages

pypet

python wrappers for rusts petgraph

scripts

A collection of scripts related to neural circuit analysis and image processing for python, Fiji, TrakEM2, CATMAID, and others.