Labeling divided cells on other types of heatmaps?

Image Analysis
#1

Hi all,

I’m wondering whether there’s a way to highlight/label divided cells on other types of heatmaps in MGX? Once I labeled the parents on the image of the 2nd time-point based on the 1st time-point, I was able to generate separate heatmaps of cell proliferation and growth or PDG on the 2nd time-point sample. However, it will be much easier visually if I can directly highlight the divided cells on the growth/PDG heatmaps, especially we are trying to disentangle the effects of cell proliferation vs. expansion on growth.

Thank you very much!

Minya

#2

How do you want to highlight them? If you just want to see the cells that have divided, you can change the transparency in the second time point so that the signal shows through, like in the attached image.

Transparent
Transparent1279×964 124 KB

Another option might be to write a plugin to select the boundary vertices of the cells that have divided, and then use the mesh “Selected” visualization to outline them.

#3

Thank you very much for your reply!! I’m not entirely sure which cells are divided on the attached image actually… Is it easy to write a plugin? I think having a plugin like that will make visualizing divided cells on the growth/PDG heatmaps very straightforward and easy, but I don’t know how much work this requires from the developers’ side.

Best,
Minya

#4

Hi Minya,

The only way currently to “highlight” cells in a heat map is to select them.
As you mentioned already, you can use the proliferation heat map to find the divided cells. To select them you can use the process “Mesh/Heat Map/Heat Map Select” (with Lower boundary >1 to find the cells that divided, so for instance 1.1 and the Upper boundary as high as your proliferation goes).
Now you can load whatever heat map you need (without changing the selection) and turn on the “Cells” visualization in the “Main” tab under “Mesh”. I did this here with the tomato meristem sample data:

Selection_465
Selection_465887×804 162 KB

You could also change the colors for the cells outlines (default cyan and red).

Implementationwise we could probably add an option to only show the outlines of the selected cells (and not off all cells), but this is more a question of the visualization.

Let me know if sth is not clear.
Best,
Soeren

#5

Fantastic!!! This is exactly what I needed and thank you very much for your help!!

Best,
Minya