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3dscript

aba_j

Brain atlasing toolkit for ImageJ

acsauto

ACSAuto script to semi-automatically evaluate ultrasound pictures

actionbar

Custom toolbars and mini applications with ActionBar. Proceedings of the 2nd ImageJ User and Developer conference, Luxembourg, November 6-7th, 2008. http://dx.doi.org/10.5281/zenodo.35653

adapt

FIJI Plugin for quantification of cell migration, protrusions, and fluorescence intensities

angiotool

A trial to convert AngioTool ( https://ccrod.cancer.gov/confluence/display/ROB2/Home ) into a Fiji plugin

appmode

Creating web applications with Jupyter and Binder

barcode_codec

plugin for ImageJ to Encode/Decode 1D/2D Barcode

beakerx

Beaker Extensions for Jupyter Notebook

betaseg.github.io

bigdataviewer-core

ImgLib2-based viewer for registered SPIM stacks and more

bigdataviewer-ui-panel

bigdataviewer-vistools

Helpers to use BigDataViewer as a quick visualization tool in other projects.

bigstitcher

ImgLib2/BDV implementation of Stitching for large datasets

bigtrace

FIJI plugin for tracing of curvilinear structures in volumetric microscopy datasets

bill_duncan

Repo used by Bill Duncan to test ideas. Once ideas have been sufficiently developed, a new repo should be created.

biobeam

GPU accelerated beam propagation tools for biological light tissue simulations

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.

bioimagebook.github.io

An introduction to bioimage analysis - http://bioimagebook.github.io

biojava

:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.

biovoxxel_toolbox

blind-experiment

An ImageJ plugin to assist with blind analysis of image data.

bokeh

Interactive Web Plotting for Python

bonej2

BoneJ2 - the next gen version of BoneJ in development

bug_submitter

build-a-binder.github.io

Increase the number of people publishing educational, journalistic, and scientific materials that enable readers to read, edit, re-run and re-use that content. Using mybinder.org

cellpose

a generalist algorithm for cellular segmentation

cellprofiler

An open-source application for biological image analysis

chbg

Convex Hull BG for ImageJ

clearmap2

ClearMap 2.0 with WobblyStitcher, TubeMap and CellMap