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Version: 2025.07-beta

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

Leica Laser Microdisector (LMD) XML Export​

To export Visiopharm ROIs in Leica LMD XML format, ensure you have at least three calibration points. These can be specified by using Visiopharm Text Annotations placed in three well-distributed and easily recognizable image locations. Have the text for the calibration spots being Calibration 1, Calibration 2, ..., as shown in the example image below.

Example of the three calibration points in the image.
Example of the three calibration points in the 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. This can be adjusted in Registry Editor under Computer\HKEY_LOCAL_MACHINE\SOFTWARE\Visiopharm\VPSDK as shown below.

Registry Editor showing the closing diameter setting.
Registry Editor showing the closing diameter setting.

To see which object was written to the LMD xml pass the LMD objects back as annotations to the Visiopharm overlay by enabling the option Pass Back LMD Objects in Registry Editor under Computer\HKEY_LOCAL_MACHINE\SOFTWARE\Visiopharm\VPSDK.

Registry Editor showing the Pass Back LMD Objects setting.
Registry Editor showing the Pass Back LMD Objects setting.

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.