Software

Title Author(s) Ecosystemsort descending License Rating
Labview National Instruments commercial
5
Average: 5 (1 vote)
Columbus Image Data Storage and Analysis System PerkinElmer commercial
3
Average: 3 (1 vote)
MountainsMap Digital Surf Commercial
0
No votes yet
AIR tools P. C. Hansen, M. Saxild-Hansen n.a.
0
No votes yet
MATLAB commercial
0
No votes yet
IMOD David Mastronarde, Rick Gaudette, Sue Held, Jim Kremer, and Quanren Xiong GPL
0
No votes yet
QuantCenter commercial
0
No votes yet
neuTube L. Feng, T. Zhao, and J. Kim This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International, which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed.
0
No votes yet
NeuronStudio Susan L. Wearne Principal Investigator Patrick R. Hof Co-Investigator Alfredo Rodriguez Sr. Software Engineer Doug Ehlenberger Software Engineer This software is provided "as is" and without warranties or representations, either express or implied, as to performance, merchantability, or fitness for any particular purpose and the user assumes all risks when using it. You may not decompile, disassem
0
No votes yet
Volocity commercial
0
No votes yet
KNOSSOS - 3D image visualization and annotation tool Max Planck Institute for Medical Research in Heidelberg, Germany unknown
0
No votes yet
Image Composite Editor Microsoft Research Interactive Visual Media Group Free
0
No votes yet
Amira commercial
0
No votes yet
SOAX Ting Xu free
0
No votes yet
AutoQuant commercial
4
Average: 4 (1 vote)
Vision4D commercial
0
No votes yet
Avizo commercial
0
No votes yet
FreeD Andrey P & Maurin Y Free but not open source
0
No votes yet
GNU Octave GNU
0
No votes yet
Huygens commercial
0
No votes yet
Metamorph commercial
0
No votes yet
MIATool Unknown
0
No votes yet
Definiens Developer commercial
0
No votes yet
Micro-Manager LGPL
5
Average: 5 (1 vote)
ITK-SNAP -
0
No votes yet
ImagePro commercial
0
No votes yet
ViBE-Z Olaf Ronneberger web
0
No votes yet
softWoRx 5.0 commercial
0
No votes yet
TurtleSeg: 3D Image Segmentation Software commercial
0
No votes yet
DIPimage Chris Luengo MATLAB for DIPimage, C-compiler for DIPlib free for non-profit use, licensed for profit use
5
Average: 5 (4 votes)
Aphelion ADCIS basic script, python, C++ commercial
0
No votes yet
OpenSlide Adam Goode, Benjamin Gilbert, Jan Harkes, Drazen Jukic, M. Satyanarayanan C GNU Lesser GPL, v2.1
0
No votes yet
ITK C++ Apache 2.0
5
Average: 5 (1 vote)
Pandore Clouard et. al. C++ Original
0
No votes yet
VolViewer Jerome Avondo C++ Creative Commons Public license
0
No votes yet
RapidSTORM Steve Wolter, Sven Proppert, Sarah Aufmkolk, André Lampe, Teresa Klein C++ Unknown open-source
0
No votes yet
CellTrack Ahmet Sacan, Hakan Ferhatosmanoglu, and Huseyin Coskun C++ GPL
0
No votes yet
Neurolucida C++ commercial
0
No votes yet
3D Slicer Steve Pieper, Ron Kikinis C++ a BSD-style open source license
0
No votes yet
Aquiarium Pavel Matula C++ GPL
0
No votes yet
ASAP Geert Litjens C++ GPL2
0
No votes yet
SR-Tesseler Florian Levet, Jean-Baptiste Sibarita C++ GPLv3
0
No votes yet
OpenCV C++ BSD
0
No votes yet
Auto-Bayes Yunqing Tang, Johnny Hendriks, Thomas Gensch, Luru Dai & Junbai Li C++ BSD and LGPL
0
No votes yet
v3dlib Petr Matula C++ LGPL
0
No votes yet
FARSIGHT C++ / Standalone GPLv2, and Apache 2.0
0
No votes yet
XuvTools Mario Emmenlauer, Aaron Ponti, Olaf Ronneberger C++, Java GNU General Public License v2
0
No votes yet
VIGRA Ullrich Koethe and many contributors C++, Python, Matlab (part only) MIT
5
Average: 5 (2 votes)
Vaa3D Hanchuan Peng C++, Qt MIT License
0
No votes yet
PRIISM/IVE IVE development team C/C++, FORTRAN Custom
0
No votes yet
WIS-NeuroMath Ofra Golani, Meirav Galun, Ida Rishal, Michael Fainzilber compiled Matlab free for non-profit use
5
Average: 5 (1 vote)
WIS-PhagoTracker Ofra Golani, Meirav Galun, Suha Naffar Abu-Amara , Benjamin Geiger Compiled Matlab free for non-profit use
5
Average: 5 (1 vote)
OpenMOLE Romain Reuillon, Mathieu Leclaire, Jonathan Passerat-Palmbach extension of Scala AGPLv3 free software license
0
No votes yet
simpleElastix Kasper Marstal ITK Apache
0
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ImageJ Wayne Rasband Java Public Domain
0
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ImageJFX KnopLab Heidelberg, Cyril Mongis Java GPL
0
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Bio7 Dr. Marcel Austenfeld Java EPL, an OSI approved OpenSource license
0
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SIMcheck Graeme Ball and Lothar Schermelleh JAVA GPL
0
No votes yet
Endrov Johan Henriksson Java BSD 3-Clause, GPL
0
No votes yet
fairSIM Marcel Müller Java GPL
0
No votes yet
WormGUIDES The WormGUIDES app is developed and maintained by the laboratories of Dr. Zhirong Bao and Dr. William Mohler. Major contributors of the desktop app include Doris Tang (New York University), Braden Katzman (Columbia University) and Dr. Anthony Santella of the Bao Laboratory. For questions or comments contact support@wormguides.org. Java unknown
0
No votes yet
MicrobeJ Adrien Ducret, Yves Brun, Ellen Quardokus Java unknown
0
No votes yet
ThunderSTORM M. Ovesný, P. Křížek, J. Borkovec, Z. Švindrych, G. M. Hagen Java GPL
0
No votes yet
SuReSim Varun Venkataramani, Frank Herrmannsdörfer, Mike Heilemann and Thomas Kuner Java GNU GPLv3
0
No votes yet
Fiji Java GPL v2 (and others: http://fiji.sc/Fiji:About)
5
Average: 5 (1 vote)
ImgLib2 Stephan Saalfeld, Stephan Preibisch, Tobias Pietzsch, Curtis Rueden, Barry DeZonia, Christian Dietz, Martin Horn, Mark Hiner, et al Java BSD
0
No votes yet
Icy Fabrice de Chaumont and Stephane Dallongeville Java GPLv3
0
No votes yet
SynPAnal Eric Danielson, Sang H. Lee Java GPL
0
No votes yet
KNIME Image Processing and Analysis Java, Eclipse GPL
5
Average: 5 (1 vote)
QuPath Peter Bankhead Java, Matlab GPL3
0
No votes yet
Cytomine Raphaël Marée, Loïc Rollus, Benjamin Stévens, Renaud Hoyoux, Gilles Louppe, Rémy Vandaele, Jean-Michel Begon, Philipp Kainz, Pierre Geurts and Louis Wehenkel Java, Python Apache2
0
No votes yet
Phenoripper Satwik Rajaram, Benjamin Pavie, Lani F Wu & Steven J Altschuler MATLAB GNU General Public License
0
No votes yet
u-track LCCB MATLAB GPL
0
No votes yet
Advanced Cell Classifier Peter Horvath Matlab GNU GPL version 3
0
No votes yet
easyFRAP Maria Anna Rapsomaniki, Panagiotis Kotsantis, Ioanna-Eleni Symeonidou, Nickolaos-Nikiforos Giakoumakis, Stavros Taraviras and Zoi Lygerou Matlab GPL
0
No votes yet
CellSegm Erlend Hodneland Matlab GNU General Public License
0
No votes yet
GelBandFitter Kenneth S. Campbell and Mihail I. Mitov, University of Kentucky Matlab N/A (available at no cost to academic users)
0
No votes yet
SIMToolbox Pavel Křížek, Tomáš Lukeš, Martin Ovesný, Karel Fliegel, and Guy M. Hagen MATLAB GPL
0
No votes yet
PALMsiever Thomas Pengo, Seamus Holden MATLAB GPL
0
No votes yet
Balanced SOFI Marcel Leutenegger MATLAB GNU General Public License version 3
0
No votes yet
Clus-Doc Sophie V. Pageon, Philip R. Nicovich, Mahdie Mollazade, Thibault Tabarin, Katharina Gaus MATLAB Unknown
0
No votes yet
FOCAL A. Mazouchi, JN. Milstein MATLAB Unknown
0
No votes yet
SimuCell Matlab free ?
0
No votes yet
Matlab Image Processing Toolbox Matlab commercial
5
Average: 5 (1 vote)
Matlab Computer Vision System Toolbox Matlab commercial
0
No votes yet
Schnitzcells Matlab registration required
5
Average: 5 (1 vote)
IceImarisConnector Aaron Ponti MATLAB, python GNU Public License version 2.0
0
No votes yet
Colormine ColorMine.org Nuget MIT
0
No votes yet
Huygens Remote Manager Volker Baecker, Aaron Ponti, Asheesh Gulati, Alessandra Griffa, José Viña, Daniel Sevilla, Niko Ehrenfeuchter, Torsten Stöter, Olivier Burri PHP, Python, Tcl, MySql, PostgreSQL, apache2 CeCILL license
0
No votes yet
jicbioimage Tjelvar S. G. Olsson​, Matthew Hartley Python MIT
0
No votes yet
Ctrax - Caltech Multiple Fly Tracker Kristin Branson, Alice A Robie, John Bender, Pietro Perona & Michael H Dickinson Python ?
0
No votes yet
scikit-image Stéfan van der Walt, Johannes L. Schönberger, Juan Nunez-Iglesias, François Boulogne, Joshua D. Warner, Neil Yager, Emmanuelle Gouillart, Tony Yu and the scikit-image contributors. Python BSD
0
No votes yet
MyTardis http://www.mytardis.org Python Apache v2
0
No votes yet
pythonxy pierre.raybaut, grizzly.nyo Python GPL v3
0
No votes yet
PopulationProfiler Matuszewski, D. J., Wählby, C., Puigvert, J. C., Sintorn, I.-M. Python BSD-3-clause
0
No votes yet
CellCognition Held Michael, Thomas Walter, Sommer Christoph, Rudolf Hoefler Python GPLv3
5
Average: 5 (1 vote)
CATMAID Stephan Saalfeld, Albert Cardona, Volker Hartenstein, Pavel Tomančák Python GPL3
0
No votes yet
ilastik Python GPLv2
5
Average: 5 (1 vote)
python-javabridge Vebjorn Ljosa, Lee Kamentsky, Johannes Schindelen Python BSD
0
No votes yet
python-bioformats Lee Kamentsky, Vebjorn Ljosa Python GPL
0
No votes yet
PINK Laszlo Marak, Hugues Talbot, Michel Couprie Python / C++ / C CeCILL (GPL Compatible)
0
No votes yet
Mahotas Luis Pedro Coelho Python numpy MIT
5
Average: 5 (1 vote)
BioImageXD Pasi Kankaanpää, Lassi Paavolainen, Varpu Marjomäki, Jyrki Heino Python, C++ GNU General Public License v2
0
No votes yet
Lama: The LocAlization Microscopy Analyzer Sebastian Malkush, Mike Heilemann Python, Cython, C GPLv3
0
No votes yet
CellProfiler Lee Kamentsky Python, Java GPL
5
Average: 5 (2 votes)
OMERO OME Consortium; http://www.openmicroscopy.org/site/about/who-ome Python, Java, C++ GPL v2
0
No votes yet
imageHTS Gregoire Pau, Xian Zhang, Michael Boutros, Wolfgang Huber R LGPL-2.1
0
No votes yet
EBImage Andrzej Oleś, Gregoire Pau, Mike Smith, Oleg Sklyar, Wolfgang Huber, with contributions from Joseph Barry and Philip A. Marais R LGPL
0
No votes yet
Imaris Bitplane Standalone commercial
0
No votes yet
ISE-MeshTools Renaud Lebrun vtk, c++ GNU General Public License v2
0
No votes yet
Visiopharm Visiopharm Web browser Commercial
0
No votes yet