BioWes – Aquatic organism behavior analysis   BioWes – Image analysis and representation   BioWes – Visualization framework 

 FISCEAPP 

The study was financially supported by the Ministry of Education, Youth and Sports of the Czech Republic - projects „CENAKVA“ (No. CZ.1.05/2.1.00/01.0024), “CENAKVA II“ (No. LO1205 under the NPU I program)

BioWes – Aquatic organism behavior analysis

Software is a part of a complete solution for the management of experimental data and metadata. Software is a plug-in for processing of experimental data, which is executed directly from the Protocol manager and directly accesses the data in the protocol.

Software performs detection and tracking of objects (fish) in medium size tanks. The input of the program are pictures from the IR camera placed above the tank. The camera captures events in the tank with the sampling frequency of 10 fps. Software estimates the background by calculating the mean and variance of each pixel of the image, along with continuous updates this value during the changes of background or tank illumination. Based on the knowledge of the background objects are detected using background subtraction for each frame. Subsequent application of methods of tracking and objects filtering according to given parameters produce as output short 3D trajectory of fish in the tank. Software can be used to analyze the behavior of fish shoals in the case of various experiments with conditions or fish feeding or as an early warning system in case of abnormal behavior of fish.

Manual

Binary Software License BioWes – Aquatic organism behavior analysis

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BioWes – Image analysis and representation

Software is part of a complex solution for the management of experimental data and metadata. Software is a plug-in for image processing, which is run directly from the Protocol Manager and directly accesses the data protocol.

Software performs conversion of image data based on information theory, which leads to suppression of unwanted information in the image (noise) and signal enhancement. Software is used to improve image data to detect objects in a scene by human expert or by an automatic computer vision methods. The enhanced image is used to calculate a unique image descriptors (PIG) which is used for classifying of the image data. Unique identifier PIG can then be used for classifying image data divided into classes. A concrete example is the use of image processing of light microscopy images, which is used to classify the different stages of cell division. The input of the program is an image or series of images, and outputs is the modified image and value of PIG descriptor. Advantage of the software is the minimum number of parameters that must be set by the user. With one variable the user can define what part of the information in the resulting image will be suppressed or emphasized.

Manual

Binary Software License BioWes – Image analysis and representation

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BioWes – Visualization framework

The Software is a part of a complete solution for the management of experimental data and metadata. Visualization framework is a versatile tool for creating specialized visualization modules that perform display of raw experimental data such as friction, scatter plot, the correlation plot. Software includes a demonstration module to display a trend of measured data for fish mortality for a particular experiment.

Visualization framework has defined user interface that enables the creation of plug-ins from third parties, which then can be used in the system BioWes. Framework provides functions to access protocols and data (experimental data + metadata) through which it can proceed to the protocols according to the user's privileges.

Manual

Binary Software License BioWes – visualization framework

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FISCEAPP

Software allows you to performan evaluationof colorfrom recording mediasuch asdigital SLRcamerasmostly. Softwarewill detectwhatthe background isand what ismeasuredandanalyzed object(fish) andsegmentingbackgroundfrom the objectto be ableto analyze thecolorof the sample. Softwareitselfcomputes the values ofbrightness, saturation and hue, includingstandard deviations. Alsoapproximatesthe value ofthe dominant wavelengthof visible lightaccording to the standardCIE L.a.b. For the comparison of color distributions of various experiments and different color spaces (RGB, CIE L*a*b*) the comparable semi-equidistant binning of multi channels representation is introduced.

Binary Software License FISCEAPP

Download - FISCEAPP - for download send email to macho(a)frov.jcu.cz

the software is stand onle, for the correct run is need runtime compiler