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  • Working with microscopy data in openBIS ELN-LIMS
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This manual page shows how to work with microscopy data registered with the Annotation Tool.

The experiment viewer was integrated into ELN-LIMS. Each file registered to a given experiment is represented in the viewer by a thumbnail.


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Tags are listed in the Parents table as entities of type ORGANIZATION_UNIT.

Clicking on a file name in the experiment viewer or selecting the file name in the tree on the left leads to the dedicated viewer.

Click to enlarge.


The Microscopy Viewer allows previewing the file in the browser. One can choose the file series of interest (for example, a given stage position or a given well) in the Data set pull-down menu and control the display of its Channels: in composite mode, specific channels can be turned on and off, or individual channels can be displayed. By default, the various channels are displayed with optimal image contrast at a default resolution, but those can be adapted using the Filter and Resolution fields. In case of multiple planes or time points, the Time and Depth sliders are activated.


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