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abfload

matlab fuction for reading abf files including v2.0 files

alignment_projects

Aligner for large scale serial section image data

allensdk

code for reading and processing Allen Institute for Brain Science data

arduino

open-source electronics prototyping platform

atfijijavaplugins

These are java plugins I wrote to make use of existing plugins/features of FIJI to automate the Array Tomography reconstruction process. It assumes files are laid out in the format given by our ZVIunpack scripts, or MosaicPlannerLive.

autouc7

Arduino code for programatic interfacing with Leica UC 7 via mouse emulation

charts

Helm Charts

chunkflow

Compose chunk operators to create pipeline for distributed computation

cloud-volume

A client for reading and writing Neuroglancer Precomputed volumes on cloud services.

cudasift

A CUDA implementation of SIFT for NVidia GPUs

czifile

czi reader from https://www.lfd.uci.edu/~gohlke/code/czifile.py.html

dash-connectivity-viewer

diced-docker

a repository demonstrating diced running in docker

dl-docker

An all-in-one Docker image for deep learning. Contains all the popular DL frameworks (TensorFlow, Theano, Torch, Caffe, etc.)

dracopy

Python wrapper for Google's Draco mesh compression library

dynamicannotationdb

em_aligner

A set of tools to assist in aligning (registering) large numbers of EM images into a coherent image volume in two and three dimensions.

em_aligner_python

Python version of Khaled Khairy's EM_aligner, supporting distributed assembly and solve

embinder

a test of producing a binder with access to minnie data

euclidean-distance-transform-3d

Multi-Label 3D Anisotropic Euclidean Distance Transform (MLAEDT-3D). Useful for dense biomedical image segmentations.

example-python

Python coverage example

fiji

Fiji Is Just ImageJ

gamer

Geometry-preserving Adaptive Mesh Generator

gitignore

A collection of useful .gitignore templates

hbpallentest

Testing out using Binder to share Allen ipython notebooks at HBP conference

igneous

Python pipeline for Neuroglancer compatible Downsampling, Mesh, Remapping, and more. Originally by Nacho and Will.

kubernetes-ingress-controller

Kong for Kubernetes

labelops

Operates on labeled neuronal meshes.

makeat

A makefile style workflow for automating Array Tomography Reconstruction

marshmallow-jsonschema

JSON Schema Draft v4 (http://json-schema.org/) formatting with marshmallow