Search Results for "software open-source"
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Showing 12 open source projects for "software open-source"
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ReViMS
ReViMS, a 3D volume rendering tool for light-sheet/confocal microscopy
Reconstruction and Visualization from Multiple Sections (ReViMS), an open-source, user-friendly software for automatically estimating volume and several other features of 3D multicellular aggregates (i.e., cancer spheroid, zebrafish, fruit fly). ReViMS requires a z-stack of 2D binary masks, obtained by segmenting a sequence of fluorescent images acquired by scanning the aggregate along the z axis, using a confocal or a light-sheet fluorescent microscope. -
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ReViSP
ReViSP, a 3D volume rendering MATLAB tool for multicellular spheroids
Reconstruction and Visualization from a Single Projection (ReViSP) tool: a 3D volume rendering method we developed to reconstruct the 3D shape of multicellular spheroids, besides estimating the volume by counting the voxels (3D pixels) fully included in the 3D surface. ReViSP is written in MATLAB (The MathWorks, Inc., Massachusetts, USA) and the source code is freely provided. Requirements for running ReViSP from the source code: MATLAB 2020a and Image Processing Toolbox 11.1 or later versions. Please, when using this software, cite these articles: (a) F. Piccinini, et al., Cancer multicellular spheroids: Volume assessment from a single 2D projection. Computer Methods and Programs in Biomedicine, 118(2):95–106, 2015. ... -
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PRMLT
Matlab code of machine learning algorithms in book PRML
This Matlab package implements machine learning algorithms described in the great textbook: Pattern Recognition and Machine Learning by C. Bishop (PRML). It is written purely in Matlab language. It is self-contained. There is no external dependency. This package requires Matlab R2016b or latter, since it utilizes a new Matlab syntax called Implicit expansion (a.k.a. broadcasting). It also requires Statistics Toolbox (for some simple random number generator) and Image Processing Toolbox (for... -
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TracTrac
Massive Object Tracking Software (Matlab/Python)
TracTrac is a Particle Tracking Velocimetry (PTV) software which is extremely fast (more than 10k points tracked per second, 100k under python) and accurate (up to 0.01 pixel resolution), forming thus a good concurrent to the state-of-the art PIV/PTV algorithms. It allows to track anything that moves: birds, ants, grains, water flows... It runs on Python (v2&3) or Matlab (>2012a with Image Processing toolbox). Give it a try ! Get the last sources on GitHub:... -
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F-Tracker3D
A software tool for tracking fluorescent cells in 3D
F-Tracker3D is acronym of "fluorescent cell tracker in three-dimensions". It is a software tool designed to track fluorescent cells using time-lapse z-stacks of images acquired with a confocal or light-sheet microscope. First, each single cell is tracked in 2D by using the maximum intensity projections of the z-stacks and CellTracker, the free open source software available at: www.celltracker.website. Then, the 3D track of each cell is obtained analysing the z-stacks and looking for the z-plane with the maximum intensity value for the different x-y positions previously determined. ... -
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GridMos
GridMos, mosaicing tool (in MATLAB) to improve cell counting.
...However, performing the cell counting by tagging the cells in a steady image mosaic increases the reliability of the counts performed. Unfortunately, to build a mosaic of a hemocytometer's grid shows some problem due to the repeated patterns (i.e., the squared blocks of the grid). GridMos is an open-source software tool conceived to build an image mosaic of a hemocytometer's grid. It is optimized to build the mosaic starting from a sequence of overlapping images previously acquired. The Graphical User Interface (GUI) implemented makes GridMos a very user-friendly software tool. Requirements: MATLAB 2009b (32-bit) and Image Processing Toolbox 8.1 or later versions. -
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matImage
An image processing and analysis library for Matlab
MatImage is a Matlab library for image processing and analysis in 2D and 3D. It contains more than 250 fonctions for image enhancement, filtering, analysis, or visualisation, as well as for creating basic test shapes. It is built as a complement of the Mathworks image processing toolbox (IPT). Project is being transfered to GitHub: http://github.com/dlegland/matImage -
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MatrixUser
A Multi-functional GUI-based Program for Image Processing and Analysis
The MatrixUser project is moving to GitHub, the latest version can be obtained from https://leoliuf.github.io/MatrixUser/ Most of the medical images (e.g. CT, MRI, PET, etc.) comprises multiple frames which represent slices, phases, timing etc. from the same imaging object. Those images can be saved as multidimensional matrices in Matlab thanks to Matlab's powerful support of multidimensional data representation. However, within Matlab, most of image manipulation functions are limited or... -
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This package can be used for further development of package needs to deal with 3D geometrical relationship. It provides class for Vector, Point, Coordinate, transformations and also provides functions for dealing with relationships between them.
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Software Defined StorageQuantaStor is a unified Software-Defined Storage platform designed to scale up and out to make storage management easy while reducing overall enterprise storage costs.
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golib
C++ collection mostly for image processing
libGo is a C++ class library containing all kinds of things that proved useful to me. Included are: - Linear algebra, using LAPACK and CBLAS - V4L(1) image grabber - Multithreading - Image containers (up to 3D) - Some simple optimisation code - Python embedding helper - Matlab interface - .. and other things, have a look at the HTML documentation! golib grew over many years, things I had use for have been added now and then. Some parts are better taken care of than others. If... -
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im-browser
MIB is a high-performance software package for image segmentation
Microscopy Image Browser (MIB) is a high-performance software package for advanced image processing, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets. Home page: http://mib.helsinki.fi
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