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Adjust Image Colors

openBIS has been integrated with the Image Color Adjustment tool written by Adam Srebniak from the SyBIT team.
To use it go to the plate layout, click on the well and press the "Adjust Colors" button:

An application in a separate window will be launched, it may take a while for the first time.
Before the first launch a window will be displayed asking you to allow the tool to run on your computer. You have to click "Allow":

Then you can change the colors using different Lookup Table transformations (LUT), and adjusting brightness and contrast:

Click "Apply" to save the settings. The changes affect all images in the experiment when you browse them in openBIS!
You can always undo the changes by launching the tool again, unclicking the LUT button and resetting Brightness/Contrast settings.

LUT transformations work well only for single channels, at the moment we discourage to use them for "Merged Channels".

This tool is still being improved. Very soon the "reset" button will be added and the preview of the edited image will be made bigger.

Visualize value of any feature on a heatmap

If the image analyses are imported to openBIS you can easily visualize them as a heatmap.
Just go to the plate layout view and choose the feature of interest, e.g. "Infection Index", in the "Choose heatmap kind" dropdown list.
You will see a heatmap showing the distribution of the infection index on the plate. Hold the mouse cursor over a well to see the exact value of the infection index for the well. Click on the well to see the images.

Import any type of screen

There are no restrictions on well metadata. Metadata from compound screens or pooled siRNA screens can be imported:

Browse annotated data

From the plate layout a distinguished feature as shown in the heatmap strikes you. Upon clicking on the well a new windows opens where you can browse based on the gene or siRNA information for the associated metadata, images and analysis results across the whole experiment.

Metadata + Images + Analysis results of wells based on the content, such as gene, siRNA or compound:

Screening Library Index

Any material used in a screen can be listed, e.g. all genes, siRNAs or compounds used in a RNAi or Chemical Compound screen, respectively:

Search by any attribute

Search for metadata, images and analysis results based on gene symbols, compound names or parts of an annotation you added:

Compare data across all experiments

E.g. show all images and feature vectors for gene SIGMAR1 across all experiments stored in openBIS

Store 10000 times less files on the hard disk

Store original images and thumbnails of one plate in HDF5 container.
Fast access to single files. Compression possible. Admin friendly.

Other improvements

  • Extended API, MatLab access
  • Simplified user interface (flexible way of re-configuring the openBIS web client)
  • Filter images by analysis results
  • Performance improvements
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