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aba_j

Brain atlasing toolkit for ImageJ

abapi-jclient

Java client for the Allen Bain RESTful API

bigdataviewer-bioformats

Opens bioformat images in BigDataViewer

bigdataviewer_scijava

Scijava commands for starting BigDataViewer and exporting data.

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. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.

hcs-webinar-notebooks

Jupyter notebooks from our OMERO Plus for High Content Screening & Analysis webinar

hrm_installer

Set of bash scripts for the automated installation and setup of the Huygens Remote Manager.

ij-command-1

ij-command-2

imglib2

A generic next-generation Java library for image processing

intellij-ij-scripting

Code in IntelliJ, run in Fiji (is just ImageJ)

knime-rgg

scripting templates for the KNIME scripting integrations

mandelbrot-set-explorer

An interactive Mandelbrot set, made with Python3 and Tkinter

matconsolectl

Control MATLAB from Java, forked from matlabcontrol

matlabcontrol

matlabcontrol is a Java API that allows for calling MATLAB from Java. You can eval, feval, as well as get and set variables. Interaction can be performed from either inside MATLAB or outside MATLAB.

nanozoomer-j

ImageJ plugin for handling NDPI files.

ome-documentation

Sphinx-based documentation for the Open Microscopy Environment

omero-user-scripts_unifr

Plugins for OMERO

openmicroscopy

OME (Open Microscopy Environment) develops open-source software and data format standards for the storage and manipulation of biological light microscopy data. A joint project between universities, research establishments and industry in Europe and the USA, OME has over 20 active researchers with strong links to the microscopy community. Funded by private and public research grants, OME has been a major force on the international microscopy stage since 2000.

pattern-recognition-2016

swissbias.github.io

Website for the SwissBIAS network: Swiss BioImage Analysts' network