Search Results for "c source code"

...It provides a number of tools for: (a) segmenting z-stacks of fluorescence images; (b) reconstructing the 3D surface of the aggregates and estimating several features (including the volume). ReViMS is written in MATLAB (The MathWorks, Inc., Massachusetts, USA). It is an open-source tool and the source code is freely available at: http://sourceforge.net/p/revims Requirements: MATLAB R2017b and Image Processing Toolbox 10.1 or later versions.

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. ...

...The tool requires as input the original RGB images, and the FastRed, FastBlue, DAB channel, easily obtained using the Fiji function: "ImageJ" -> "Image" -> "Colour Deconvolution" -> "FastRed FastBlue DAB" Then, the tool first segment the nuclei using the FastBlue channel and the DAB channel, and then computes statistics by subdividing the sample in three regions according to the FastRed channel: a dark-red ROI, a light-pink ROI and a white ROI. ANDTool is written in MATLAB (The MathWorks, Inc., Massachusetts, USA) and the source code and standalone versions are here available for download. USER MANUAL: see the specific PDF available in the Files section. REQUIREMENTS: MATLAB R2017b and Image Processing Toolbox 10.1 or later versions. MAIN CONTACT: Filippo Piccinini (E-mail: filippo.piccinini85@gmail.com)

...The code is extremely compact. Minimizing code length is a major goal. As a result, the core of the algorithms can be easily spotted. Many tricks for speeding up Matlab code are applied (e.g. vectorization, matrix factorization, etc.). Usually, functions in this package are orders faster than Matlab builtin ones (e.g. kmeans). Many tricks for numerical stability are applied, such as computing probability in logrithm domain, square root matrix update to enforce matrix symmetry.

...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. F-Tracker3D is written in MATLAB (©, The MathWorks, Inc., Massachusetts, USA) and the source code is freely provided. ...

Image Processing/Tracking Software for off-line analysis of Field Biology Videos/Recordings.

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!