Dealing with multi-cell images

The default workflow asssumes that the image contains only a single cell. In many cases however the field of view might contain multiple cells. In that case, the plugin offers a way to indicate which cell should be processed. We use here again the data from this Zenodo repository (Eike K Mahlandt, Sebastián Palacios Martínez, Janine JG Arts, Simon Tol, Jaap D van Buul, Joachim Goedhart (2023) Opto-RhoGEFs, an optimized optogenetic toolbox to reversibly control Rho GTPase activity on a global to subcellular scale, enabling precise control over vascular endothelial barrier strength eLife 12:RP84364 https://doi.org/10.7554/eLife.84364.3).

First we import the data:

Now we need to segment the cells. Obviously, both convpaint and cellpose will segment all cells if we don’t specify which cell to focus on.

At the bottom of the segmentation tab, there is an option for Select cell. If this is selected, a new Points layer is added to the viewer containing a single point at the first time point. It’s location will indicate to the plugin which cell to analyse:

By selecting the arrow tool you can move the point to the cell you want to analyze.

When we then go the the segmentation step, everything works as usual, except that only the marked cell will be processed e.g. via the convpaint plugin: