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Protocols

SciXMiner specifications

Information


Unique identifier OMICS_28945
Name SciXMiner
Alternative name Gait-CAD
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages MATLAB
License GNU General Public License version 3.0
Computer skills Medium
Stability Stable
Maintained Yes

Subtool


  • EmbryoMiner

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Versioning


No version available

Maintainer


  • person_outline Ralf Mikut

Publications for SciXMiner

SciXMiner citations

 (6)
library_books

The rumen microbiome: an underexplored resource for novel antimicrobial discovery

2017
PMCID: 5711939
PMID: 29214045
DOI: 10.1038/s41522-017-0042-1

[…] luorescence readings (excitation/emission spectra of 560/590 nm) after the addition of resazurin dye (100 µm final concentration). The results from the screen were analysed using the MATLAB extension Gait-CAD as previously described. Concentration values with a 75% reduction of luminescence or fluorescence (IC75) in relation to untreated controls were computed. Three peptide activity classes: acti […]

call_split

Fuzzy based propagation of prior knowledge to improve large scale image analysis pipelines

2017
PLoS One
PMCID: 5667823
PMID: 29095927
DOI: 10.1371/journal.pone.0187535
call_split See protocol

[…] ect correspondences of detected objects over time in all acquired images. For illustration purposes, a straightforward nearest-neighbor tracking approach implemented in the open-source MATLAB toolbox SciXMiner was used [, ]. Each object present in a frame was associated with the spatially closest object in the subsequent frame. This procedure was applied to every frame of the data set in order to […]

library_books

A New Feedback Based Method for Parameter Adaptation in Image Processing Routines

2016
PLoS One
PMCID: 5072585
PMID: 27764213
DOI: 10.1371/journal.pone.0165180

[…] A benchmark data set (https://sourceforge.net/projects/gait-cad/files/Benchmarks/hardware_items/) is specifically designed to conform to evaluation criteria that are most suitable for our methodology. A complete description of data set is given in []. It […]

call_split

Zebrafish biosensor for toxicant induced muscle hyperactivity

2016
Sci Rep
PMCID: 4815012
PMID: 27029555
DOI: 10.1038/srep23768
call_split See protocol

[…] andard deviation of intensity values were extracted from the linearized and cropped original image. All algorithms were implemented in MATLAB as an extension package to the open-source MATLAB toolbox Gait-CAD. To evaluate whether there is an effect of a test chemical on the hspb11 reporter level, the differences of the hspb11 reporter level among doses including solvent control were examined by on […]

library_books

A Benchmark Data Set to Evaluate the Illumination Robustness of Image Processing Algorithms for Object Segmentation and Classification

2015
PLoS One
PMCID: 4508044
PMID: 26191792
DOI: 10.1371/journal.pone.0131098

[…] egarding accuracy and robustness. The sources for the image processing routine, the robustness measures and the data set as well are freely available and downloadable https://sourceforge.net/projects/gait-cad/files/Benchmarks/hardware_items/. […]

library_books

Phenotype Classification of Zebrafish Embryos by Supervised Learning

2015
PLoS One
PMCID: 4289190
PMID: 25574849
DOI: 10.1371/journal.pone.0116989

[…] entrations using images of treated embryos by extracting image features (e.g. variance of pixel values) to distinguish two very obvious classes, dead or alive embryos. Classification using the Matlab Gait-CAD toolbox was shown to be in good correlation with that from experts [], however more complex defects were not addressed. Another work describes a way to automatically obtain images of zebrafis […]

Citations

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SciXMiner institution(s)
Karlsruhe Institute of Technology (KIT), Institute for Applied Computer Science, Karlsruhe, Germany
SciXMiner funding source(s)
Supported by the German Research Foundation DFG (RM, JS, Grant No MI 1315/4, associated with SPP 1736 Algorithms for Big Data) and the Helmholtz Association in the programs BioInterfaces in Technology and Medicine (BS, MTr, TA, CS, AB, KL, DB, MTa, AYK, JCO, US, RM) and Science and Technology of Nanosystems (GUN).

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