Open Microscopy Environment

Hi all,

I'm looking at using Will's "Dataset to Plate.py" script to convert a pile of TIFF images exported from a plate acquisition back into a plate format in OMERO. There are 4 fields acquired per well which the script currently does not handle. The files are exported with a naming scheme that looks like:
PlateESCH_Aug1_WellA01_Seq0000xy1.tif
PlateESCH_Aug1_WellA01_Seq0000xy2.tif
PlateESCH_Aug1_WellA01_Seq0000xy3.tif
PlateESCH_Aug1_WellA01_Seq0000xy4.tif
PlateESCH_Aug1_WellA02_Seq0001xy1.tif
PlateESCH_Aug1_WellA02_Seq0001xy2.tif
PlateESCH_Aug1_WellA02_Seq0001xy3.tif
PlateESCH_Aug1_WellA02_Seq0001xy4.tif
PlateESCH_Aug1_WellA03_Seq0002xy1.tif
PlateESCH_Aug1_WellA03_Seq0002xy2.tif
PlateESCH_Aug1_WellA03_Seq0002xy3.tif
PlateESCH_Aug1_WellA03_Seq0002xy4.tif
etc ....

and the final xy[1-4] denotes the field number so it should be relatively easy to add the field capability to the script. Has anyone done this already?

Thanks,
- Damir

Hi Damir,

I don't know of anyone who has extended the script to handle wells.
Glencoe software have a couple of HCS scripts, but they don't cover this use-case. https://github.com/glencoesoftware/omer ... cs_scripts

If all your image names are nicely ordered as you show, then it shouldn't be too hard to add a field count.

I don't know if you have to manually set 'well_index' on each WellSampleI or if that will be handled automatically by:

Code: Select all

well.addWellSample(ws)


Let us know how you get on, and if you're happy for us to merge your work back into the scripts repo, please open a PR.

Thanks,

Will.