Imaging data are the images produced by microscopy of cells, organelles, tissues etc and their associated metadata.


The Sanger Imaging Platform uses the OMERO software for the analysis of microscope imaging data. Storing data in OMERO is a procedure Cellular Genetics Informatics provide.

Please watch the following 10min video from the The Jackson Laboratory to learn the basics of browsing and annotating images using OMERO:

OMERO uploads

Users need to get data off microscopes quickly. Choose from the following use cases on how to request your data be uploaded to Sanger’s OMERO server.

Upload OME-TIFF and NDPI

Data in OME-TIFF and NDPI format can be imported as-is provided the images have pyramids generated. Please submit a ticket with a TSV file with the following columns:

filename Name of the file (my_file.ome.tiff or my_file.ndpi)
location Path to the file folder (ie: /nfs/team123/)
omero_group OMERO group name (ie. MJ_CDB)
omero_project image_omero_project OMERO project folder name (first level folder)
omero_dataset image_omero_dataset OMERO dataset folder name (second level folder)
omero_username Image owner’s username (ie. ob1)

Upload NDPIS

NDPIS need to be processed before importing this involves merging all NDPI image for individual channels into one image. Please fill the following xlsx file and submit a ticket with it attached.



Phoenix exported tiles need to be stitched together before importing to OMERO. Please fill the following xlsx file and submit a ticket with it attached.



We can also run segmentation on your images provided you give us the following information:

input_image Full path to the image file. ie. /nfs/team123/my_file.tiff
dapi_ch DAPI channel index (default 0)
cyto_ch Cyto channel index (default '')
object_diameter Object diameter (default 35)
flow_threshold Flow threshold (default 0.5)
expand Cell border expansion ammount (default 35)
magnification Magnification level (default 20)
model_type Cellpose model type (default cyto)

Our segmentation pipeline works on GPU using Cellpose in order to produce 2D or 3D images of cells and nuclei with segmentation for downstream analysis.

If you want to run the pipeline yourslef you can do so following the instructions on GitLab