Under the Segmentation Import tab, you will be able to upload Cell Segmentation masks from outside of the Enable Cloud Platform. Once uploaded, these segmentation masks can be viewed in Visualizer and leveraged in other parts of the Analysis Toolkit, just like any Segmentation masks that are generated from within the platform.

Data formatting requirements

Currently we accept the following file format for import:

• .ome.tif / .ome.tiff
  • Single-channel grayscale image conforming to OME-TIFF spec (only single layer tiffs are supported)
  • TIFF must contain 32-bit or lower signed integer values
  • Each cell must be indicated by a single contiguous object with a uniform greyscale pixel value. Each cell’s pixel value becomes its segment/cell ID. Black/0 represents no segment. This is the standard format exported by the Mesmer segmentation tool
  • Mask image must have the same pixel width/height as the associated region.

Importing a segmentation mask

To import a new segmentation mask, you will first need to create a new Segmentation Version to associate that mask with. To begin, click the + button next to “External Segmentation Versions”. This will open the following menu, where you can enter a name for the new Segmentation version, and an optional description.

Once you have created a Segmentation Version, you will be able to upload your masks and associate them with this Segmentation Version.

Following the steps on the page, upload your masks by dragging your files into the grey box, or by clicking and selecting the masks to upload. You should upload 1 Segmentation mask file per tissue region that you are importing a segmentation for.

You will then be asked to associate each individual Segmentation mask with the relevant tissue region.

You will then be asked to select the type of mask, either “Nuclear” and “Whole Cell”.

Finally, you will be asked for information to help configure the mask:

• For Nuclear Masks
  1. Nuclear Biomarker
  2. Cell Area Threshold (Optional)
  3. Number of Dilations (Can be set to zero)
• For Whole Cell Masks
  1. Nuclear Biomarker
  2. Whole Cell Biomarker (Optional)
  3. Cell Area Threshold (Optional)

More information on these parameters can be found here.