SciXMiner Files

This archive contains sample data and macros to reproduce the examples presented in the following publication:

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  SCHOTT, B.; TRAUB, M.; SCHLAGENHAUF, C.; TAKAMIYA, M.; ANTRITTER, T.; BARTSCHAT, A.; LÖFFLER, K.; BLESSING, D.; OTTE, J. C.;  
  KOBITSKI, A. Y.; NIENHAUS, G. U.; STRÄHLE, U.; MIKUT, R. & STEGMAIER, J. 
  EmbryoMiner: A New Framework for Interactive Knowledge Discovery in Large-Scale Cell Tracking Data of Developing Embryos. 
  PLoS Computational Biology, Public Library of Science, 2018, 14(4), e1006128
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Perform the following steps to start the examples:
1. Make sure MATLAB and SciXMiner are properly installed. The latest release of SciXMiner can be obtained from https://sourceforge.net/projects/scixminer/ and general information as well as installation instructions for SciXMiner are provided in the following document: https://arxiv.org/abs/1704.03298.
   
2. Download and install the EmbryoMiner toolbox from https://sourceforge.net/projects/scixminer/files/Extension%20packages/ by extracting the archive to the "application_specials" folder of your SciXMiner installation. This extension package contains all required components of the interactive knowledge discovery framework EmbryoMiner.
   
3. Open MATLAB and start SciXMiner by typing "scixminer" in the command line window of MATLAB. If you don't see the "EmbryoMiner" entry in the menu bar, open "Extras -> Choose application specific extension packages ..." and activate the EmbryoMiner toolbox. After restarting SciXMiner, the EmbryoMiner toolbox should properly load.
  
4. Once the SciXMiner GUI opened up, you can select one of the examples from the "EmbryoMinerExamples" folder with the extension *.batch. Use the menu command "File -> Apply SciXMiner Batch File" and select the example of your choice.

5. The *.batch file automatically loads the demo projects as well as the visualization windows. Batch files can be opened in a standard text editing software, in case you're interested in the code.
   
6. Further information is provided in the readme files associated with each of the examples and in the supplementary information of the publication mentioned above.

If you have any problems or questions related to the trajectory visualization framework, please do not hesitate to write us an email (benjamin.schott@kit.edu or johannes.stegmaier@partner.kit.edu), ideally including a detailed description on how to reproduce the respective error. The software was tested and compiled on Microsoft Windows 10 using MATLAB 2019a. Releases for the other major operating systems are planned for the next release.