Windows

OpenCV

Collection
Description
OpenCV is released under a BSD license and hence it’s free for both academic and commercial use. It has C++, C, Python and Java interfaces and supports Windows, Linux, Mac OS, iOS and Android. OpenCV was designed for computational efficiency and with a strong focus on real-time applications. Written in optimized C/C++, the library can take advantage of multi-core processing. Adopted all around the world, OpenCV has more than 47 thousand people of user community and estimated number of downloads exceeding 6 million. Usage ranges from interactive art, to mines inspection, stitching maps on the web or through advanced robotics.
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OpenMOLE

Collection
Description
OpenMOLE (Open MOdeL Experiment) is a workflow engine designed to leverage the computing power of distributed execution environments for naturally parallel processes. A process is told naturally parallel if the same computation runs many times for a set of different inputs, such as model experiment or data processing… It is free software distributed under the AGPLv3 free software license.
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Find Focused Slices

Component
Description

An ImageJ plugin for selecting a plane in focus among multiple slices image stack. The algorithm uses normalized variance. A short tutorial is available in the plugin web page (above).

has topic
Bioimage informatics
has function
Image feature detection
Image validation
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NeuronStudio

Collection
Description

Neuron studio is a software package to reconstruct neurons from 3D confocal images. Reconstruction can be done manually, semi-manually or fully automatic. The images as well as the detected objects are rendered in 3D. A spine detection and classification function is also included. Results can be exported as a text file with coords of the spines. It seems that active development has stopped in 2009. NeuronStudio is being developed at the Computational Neurobiology and Imaging Center (CNIC), a research laboratory at the Neuroscience Department of the Mount Sinai School of Medicine in New York.

NeuronStudio can be used with default parameters or user-defined parameters (Fully or semi-automated).

has topic
Confocal microscopy
has function
Filament tracing
Neuron image analysis
Skeletonisation
NeuronStudio_standaloneapp_window_overview

Microtubules Tool (3D)

Workflow
Description

The tool measures the total length of the microtubules in a 3D image.

See: http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Microtubules_Tool_(3…

You can find a test image here.

has topic
Bioimage informatics
has function
Filament tracing
Image thresholding
3D microtubules
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