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  • Working with microscopy data in openBIS
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This manual page shows how to work with data registered from the supported microscopes.

The experiment viewer shows a representative thumbnail for each of the datasets registered for this experiment. A set of actions that apply to the entire experiment are listed:
  • clicking on Export to your user folder copies all files to the user's working folder (at the BSSE: S:\scuworking\openbis_export).
  • clicking on Export to your HRM source folder copies all files to the source folder of the Huygens Remote Manager for deconvolution (at the BSSE: S:\scuworking\src).
  • clicking on Download packages all files into a zip archive to be downloaded through the browser.


Click to enlarge.
Clicking on a file name leads to the dedicated viewer.

Click to enlarge.


The dataset 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.
If the automatic contrast is not satisfactory, one can manually adjust it.


The actions at the file level work in the same way as at the experiment level, but just for the selected file. In addition, the acquisition metadata can be displayed.

In order, the action buttons allow to:

  • Display the associated datasets (like configuration files): this currently is only supported for YouScope acquisitions.
  • Display acquisition metadata.
  • Export the data to your personal folder (this is optional and must be configured by an administrator).
  • Export the data to your Huygens Remote Manager source folder (this is optional and must be configured by an administrator).
  • Download the compressed dataset via the browser.


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