Export cell coordinates in histocat++

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Computational image analysis of multiplexed Imaging Mass Cytometry acquisitions
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Seb
Posts: 5
Joined: Thu Aug 01, 2019 6:21 pm

Export cell coordinates in histocat++

Post by Seb » Wed Aug 07, 2019 4:02 pm

hi all

I'm working with a few watershed masks generated from mcd files and I'd like to extract the coordinates of the cells highlighted in the mask.
so far here's what I do:
- right click on the mask
- extract features from mask
- select total cells
- select the resulting mask from the explorer on the right side
- go on data table

now, that has several columns including "cell_to_X", "cell_to_Y", "X" and "Y".
what does cell to X/Y actually mean?
is it correct to assume that X and Y are the coordinates?
now, how do I export them in a table? copy/paste doesn't work, and I can't find an "export" function to save the table.

thanks
Seb
Posts: 5
Joined: Thu Aug 01, 2019 6:21 pm

Re: Export cell coordinates in histocat++

Post by Seb » Wed Aug 07, 2019 4:40 pm

thank you for the quick reply.

I can get through all steps but the export, I can't find any functions/buttons/right-click menus etc to export the table.

tnx
Seb
Posts: 5
Joined: Thu Aug 01, 2019 6:21 pm

Re: Export cell coordinates in histocat++

Post by Seb » Thu Aug 08, 2019 9:04 pm

as reply to my question
after making a mask select from the top left menu "cell data"
select "data table" from the menu on the right
then select all data from the different masks
select the markers you want to export
at the bottom of the data table view there is a button "Export as TSV"
pick name and location

thanks to Raul for the help with this!
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