Skip to main content
Version: Next

Working with layer data

LayerData (ROIs, Annotations, Labels and Heatmaps) of the active image can be saved to a file and imported to other images, or processed in other programs.

Alternatively, the Regions Of Interest (ROIs) can be extracted separately to an .xml

Export layer data​

  1. Click on or on .

  2. Navigate to and select the image with the layer data to export.

  3. Click File | Export | LayerData to start the export process.

  4. Browse to the location where the file should be saved and give it an appropriate name. Select the export type and click Save to export the layer data in the selected format.

Use separate file formats depending on the layer of data to be exported. .mld exports all layer data, while .xml files extract only the ROI data.
Use separate file formats depending on the layer of data to be exported. .mld exports all layer data, while .xml files extract only the ROI data.

Supported export formats​

The following file formats are available for export in Visiopharm:

File TypeDescriptionExtension
Visiopharm Layer DataContains data layers created in Visiopharm for analysis or visualization..mld
Nanostring OME: XML AnnotationsExported annotations in XML format compatible with Nanostring OME analysis workflows..ome.xml
TIFF ImageHigh-resolution image format commonly used in microscopy and imaging software..tif .tiff
Visiopharm ROI Annotations XMLRegion of interest annotations exported as XML files for integration with other systems..xml
Visiopharm ROI to Leica LMD (Laser Microdissection) XMLExported ROI annotations in XML format compatible with Leica LMD software..xml

Export of ROIs to Leica LMD​

To export Visiopharm ROIs in Leica LMD XML format, ensure you have at least three calibration points.

These you specify by using Visiopharm Text Annotations placed in three well-distributed and easily recognizable image locations.

Example of calibration points in an image.
Example of calibration points in an image.

The export will save all non-clear ROI objects on the overlay after performing a morphological closing, followed by a simplification using one-fifth of the closing diameter. The default closing diameter is 50 μm, but this can be adjusted via:

The closing diameter can be adjusted in Registry Editor.
The closing diameter can be adjusted in Registry Editor.

To see which object was written to the LMD xml you can pass those back as annotations to the Visiopharm overlay by enabling the following option in Registry Editor:

Enable the option to see which objects were written to the LMD xml.
Enable the option to see which objects were written to the LMD xml.

Batch import layer data​

  1. Click on .

  2. Navigate to the folder to import the layer data to.

  3. Click on and select Layer data to current folder.

  4. Browse the folder containing the layer data and press Select folder.

  5. Select Import folder in the newly opened window.

The following window will appear if the data has been successfully imported.
The following window will appear if the data has been successfully imported.
The following window will appear if the data has not been successfully imported.
The following window will appear if the data has not been successfully imported.
note

The layer data files must have a file name matching the file name of the image in the study they should be imported to. This ensures that the files will be imported and attached to the appropriate images.