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Associate segmented apical cell with segmented nuclei

Choose Associate in the main pipeline interface to run this step. The cell junctions and the nuclei must have been segmented/loaded before to do this step.

Once you have separately segmented the cell (their surface) and the nuclei, this step allows to pair together cell and nuclei to define the full cell. At the end of it, you will have for each segmented cell a corresponding nuclei (indicated by its label) or none if no close enough nuclei corresponded.

You have to first run an automatic association that will try to find the best pairing (nucleus, cell) combinations. Then you will get a step to manually correct the association.

Computing association

The algorithm to do the association is the Hungarian algorithm that find an optimal pairing of nuclei and cells based on a linking cost. This cost, the distance between the nuclei and the cell is taken as the distance in 3D between the cell surface center and the nuclei center , plus the distance in the (x,y) plane between those two centers (this addition allows to penalize more for distance in XY as nuclei are more vertically below the cell surface).

The parameter distance toassociate micron defines a threshold distance (the distance3D+distance2D) above which a nucleus is considered to far to correspond to the cell. This allows to reduce the number of candidates nuclei and searching range to do the association, so increase its value speed-up the computation, but could loose some nuclei to associate.

Once the association have been computed, you obtain two new layers on the left panel, CellNuclei and CellContours that contained the cell labels and the updated cell nuclei label. The nuclei labels have been changed so that their labels match to each associated cell. Thus a nuclei and cell with the same value are associated. In general, the colors should match as well, but it is not always the case, so check the label value by hovering over the nuclei, and by right-clicking on the cell surface to get the cell label.

Manual correction

assoe

Shortcut/options
  • To see the value of a nuclei label, you can put the mouse on top of it and you will see its label on the bottom left panel (except if vispy visualisation mode is on, disable it to get the value). Or you can double-left click on it to put its value on the nucleus parameter in the CellNuc association panel.
  • Right-click on a cell to get its label and have it put to the cell parameter in the CellNuc association panel.
  • Click on Associate now to associate the nucleus with label nucleus with the cell with label cell. If another nucleus has already the same label of the cell to associate with, its value will be changed to the maximum label + 1. Shortcut: press on c to do the association. The selected nuclei should change its color and label value to the cell one.

Additional options:

  • show_cellnames add the value of each cell label in the image.
  • sync cellsNuclei synchronize the CellNuclei and CellContours layers, so that visualisation options set on one layer are also set on the second layer. This is usefull to see only one label (with the show selected option in the top left panel) in both layers at the same time.

assosync

Outputs

When the association is finished and corrected, save the two label files to be able to reload them later. By default, the cell surface will be saved in a 2D label image called _imagename_\_cells2D.tif in the results folder,the same as for the junctions segmentation. The nuclei will be saved as a 3D label stack, containing each nuclei with its associated label in a file called _imagename_\_nuclei.tif. The save also3D junctions option saves another file of the cell surface labels at their corresponding slice (z) for each cell.

Click on save association to save these files and you can click on Association done to finish this step.