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Get Images from SiLA2 Server and Send Back Results

Laboratory Data SiLA2 Life Sciences Image Processing

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This workflow demonstrates how to get raw images from a (custom) SiLA2 server, how to process the data with KNIME nodes, and how to send comuptation results back to the SiLA2 server. **IMPORTANT** This workflow requires a Java library that we have not bundled to keep the file size minimal. Please import the entire SiLA Prototype workflow group (see link below) to run this workflow. **IMPORTANT** In order to successfully run this workflow, you have to setup a custom SiLA2 server. Please follow these instructions to start it: 1. Make sure that you have at least Java 8 installed on your computer and that the according environment variables are correctly set. (You can check this in a terminal by executing “java -version”) 2. Open a terminal or commandline and execute the following command: “java -jar <path to sila-server.jar> server -p 50052 -xml <path to plate.xml> -data <path to images.zip>”. (You can figure out the paths by right clicking on the respective item in the KNIME Explorer and selecting Copy Location > Local path) 3. Make sure that you see some output like "2021-01-08 12:37:31 INFO s.l.s.SiLAServer:97 - Server started on port=50052" in the terminal. Developed by Mike Groezinger (mike.groezinger@siobra.de) and Stefan Helfrich (stefan.helfrich@knime.com).

External resources

  • BioSero
  • siobra
  • SiLA
  • sila-server.jar sources
  • SiLA Prototype workflow group

Used extensions & nodes

Created with KNIME Analytics Platform version 4.4.1 Note: Not all extensions may be displayed.
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    KNIME Base nodes Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.4.1

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    KNIME Image Processing Trusted extension

    University of Konstanz / KNIME

    Version 1.8.3

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    KNIME Javasnippet Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.4.1

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    KNIME Quick Forms Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.4.1

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