As the different shapes in the shapes layer are linked to the cells in the table, it would be fantastic if they cross-talked.
Assuming the same indexing, filtering one of the two objects could automatically filter the other one.
Even when adding a shapes layer, it would be great to have the option to retain the objects in this layer that match with the table layer.
Or when adding new shapes layer, to only retain the ones that are joined between the two shapes layers.
As the indices of cells and nuclei don't always match, I wrote code to match up different shapes layers, and match the indices. This might be interesting too!
However, not all cells will have a counterpart in every other shapes layer, and sometimes cells are binucleated, meaning two nuclei will match the same whole cell. These things should be taken into account, as they will give rise to issues along the way.
How to index the cells then will be another issue, just as adapting the labels layer.
This also brings up the issue of multiple tables. As all different stainings will give different segmentation masks and thus different gene counts, they will lead to different tables. How do we solve this? Do we add a column in the table to address this? If so, we are having cells with double indices, which might cause issues.
As the different shapes in the shapes layer are linked to the cells in the table, it would be fantastic if they cross-talked.
Assuming the same indexing, filtering one of the two objects could automatically filter the other one.
Even when adding a shapes layer, it would be great to have the option to retain the objects in this layer that match with the table layer.
Or when adding new shapes layer, to only retain the ones that are joined between the two shapes layers.
As the indices of cells and nuclei don't always match, I wrote code to match up different shapes layers, and match the indices. This might be interesting too!
However, not all cells will have a counterpart in every other shapes layer, and sometimes cells are binucleated, meaning two nuclei will match the same whole cell. These things should be taken into account, as they will give rise to issues along the way.
How to index the cells then will be another issue, just as adapting the labels layer.
This also brings up the issue of multiple tables. As all different stainings will give different segmentation masks and thus different gene counts, they will lead to different tables. How do we solve this? Do we add a column in the table to address this? If so, we are having cells with double indices, which might cause issues.