Format & Organize Segmentation

Segmentation Formats

  • Segmentation label images are required for CellTune. [Pixel values indicate the cell IDs, 0=background.]
  • Segmentation should be single TIFF format (2D)
  • Segmentation must be the same size as corresponding channel images.
  • Data type should be integer type: uint16 or uint32

    (int16 and int32 should also work)

Segmentation Organization

Segmentation can be stored in a new separate folder, we recommend /CellTune_Data/{PROJ_NAME}/Segmentations

  • Names should be {IMAGE_NAME}_segmentation_labels.tif (e.g. Control_01_FOV_1_segmentation_labels.tif)

See whole slide example in the tutorial

If your images are single TIFF directories (like the demo data). Then you can store the segmentations directly in the image folders, named segmentation_labels.tif (e.g. /CellTune_Data/{PROJ_NAME}/Images/Control_01_FOV_1/segmentation_labels.tif).