Screening Test Data

This folder contains scripts and other files for creating and curating data for a screening instance of openBIS.

Manifest

• config

  • openbis and dss system.properties files for a local instance of openbis

• etc

  • data-set-handler-microscope.py -- A python drop-box that imports microscopy images

  • data-set-handler-features.py -- A python drop-box that imports feature vectors

  • data-set-handler-splitted.py -- A python drop-box that imports plates comprised multiple single-channel images

  • data-set-handler-plate.py -- A python drop-box script for dss that imports plates and analysis data

• source

  • admin-console

    • An admin-console script that creates optional meta-data for the screening test data. Running this script is not required.

  • bash

    • create-empty-screening-db.sh
      • A script that initializes an empty screening database. This must be run to create the initial database for the test data if no database exists.

  • python

    • generate-test-plate-analysis.py -- A script that generates analysis data (csv files)

    • generate-test-plate-overlays.py -- A script that generates overlay-images for a plate

      • n.b. This script will only run on MacOS 10.5+

    • generate-test-plate.py -- A script that generates raw-images for a plate. This can be colorful images or black-and-white images for each channel.

      • n.b. This script will only run on MacOS 10.5+

    • generate-test-series.py -- A script that generates a microscopy image series

      • n.b. This script will only run on MacOS 10.5+

• exp-1-library.xls An Excel file for importing a library (defining materials and plates) to be uploaded by menu item "Administration -> General Import"

Use

Follow these instructions to use this infrastructure. It instructions assume that the screening version of openBIS is running inside Eclipse.

Initialize DB

Run the initialization script.

screening/source/bash/create-empty-screening-db.sh

This will create an initial screening database with the name used by the configuration files.

Configure Servers

1. Replace the openBIS service.properties with screening/config/openbis-service.properties
2. Replace the dss service.properties with screening/config/dss-service.properties
3. In the screening folder create the following sub-folders

• targets/platonic
• targets/platonic/store
• targets/platonic/incoming-platonic-microscope
• targets/platonic/incoming-platonic-plate
• targets/platonic/incoming-platonic-plate-features
• targets/platonic/incoming-platonic-plate-overlays
• targets/platonic/incoming-platonic-plate-splitted

Configure openBIS

1. Start openBIS and DSS and log in as admin/admin.
2. Create space PLATONIC.
3. Create project SCREENING-EXAMPLES.
4. Create an experiment EXP-1 of type HCS_PLATONIC in this project.
5. Use the Import->General Import to import the file screening/exp-1-library.xls

Generate and Register Data

Run the script screening/source/bash/generate-test-experiment.sh to generate data for the experiment.

6. Register

• PLATE-1 -> targets/platonic/incoming-platonic-plate
• PLATE-1.OVERLAY-1 -> targets/platonic/incoming-platonic-plate-overlays
• PLATE-1.OVERLAY-2 -> targets/platonic/incoming-platonic-plate-overlays
• PLATE-1.analysis1.csv -> targets/platonic/incoming-platonic-plate-features
• PLATE-1.analysis2.csv -> targets/platonic/incoming-platonic-plate-features