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backend_swing

A Java/swing backend for Matplotlib using the javabridge

bioformats

Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment (particularly UW-Madison LOCI and Glencoe Software). Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.

build-ilastik-on-windows

Build Ilastik and its dependencies on Windows using setuptools

cellh5

CellH5 is an HDF5 data format for cell-based assays in high-throughput microscopy, which stores high-dimensional image data along with inter-object relations in graphs.

cellprofiler

CellProfiler mirror of the SVN repository. Note that currently, this repository is updated manually from a git-svn clone of the official SVN repository (see Cloning_in_git.txt).

cellprofiler-analyst

Software for exploring and analyzing large, high-dimensional image-derived data.

centrosome

An open source image processing library

ceph-container

Docker files and images to run Ceph in containers

chunglab-neuroglancer-tools

Some tools for adding URLs to Leviathan and displaying them

cp-filterbank

A filter-bank plug-in for CellProfiler

example-notebooks

glayout

Graph layout using NetworkX

homebrew

The missing package manager for OS X.

homebrew-python

Python formulae for Homebrew

idm

cython version of IDM

ilastik-0.5

Interactive Learning and Segmentation Toolkit

ilastik-build-win64

CMake scripts to compile ilastik and all its dependencies on Windows 7 and 8 (64-bit)

imagej

ImageJ2: the next-generation version of ImageJ

imglib

A generic next-generation Java library for image processing

ingest-client

A Python command line application for performing distributed ingest of image data into the Boss

isbi_challenge

Code for my entry in the ISBI 2012 challenge.

keras

Deep Learning library for Python. Runs on TensorFlow, Theano, or CNTK.

keypointalign

Python application to align images using keypoints

leek-test-lfs

see if I can store a binary using git-lfs

linux-healthcheck

My personal daily health checkup on my linux box

medianprojection

Compute the median projection of an image stack.

microscoper

A simple wrapper for python-bioformats to convert .vsi CellSense format to TIFF.

multistackregistration

Modified version of MultiStackRegistration, for use from scripts.

neuroglancer

WebGL-based viewer for volumetric data

neuroproof

Tool for graph-based image segmentation and analysis