Suggestions on seeding cells in MGX?

Hi!

I’m using MGX for my meristem confocal time-lapse to analyze changes in cell proliferation and expansion, but I’m having some troubles of making seeding the cells consistently and more efficiently. All the online tutorials I found are talking about seeding cells with alt-key and the “add new seeds” tool to outline each cell, but this became a very time-consuming process when each of my samples has about 500 cells, and I have multiple replicates per stage, and multiple stages. I’m also worried about the consistency issue in my own judgment in outlining the cells, since sitting in front of the screen to outline cells for an hour made my eyes fatigue and misjudge cells.

I’m wondering whether there’s a more efficient way of seeding the cells? Any comments and suggestions will be very appreciated!

Thank you in advance!

Best,
Minya

Hi Minya,

You only need to put one seed per cell, you don’t really need to “draw” around them. The only time you need to draw is when one of the walls looks dodgy, and you are worried that the watershed will bleed into the neighboring cell.

Try it by seeding one triangle per cell, and then you will see which cells really need drawing.

So long as you stay at least a triangle inside the cell when seeding, the watershed will find the same wall, so there is no bias. This would only happen in the case where the wall had a hole in it, and you have to draw close to the wall to stop it from spilling into the next cell.

There are auto-seeding and auto-segmentation options that can work well if you get the parameters right. But then you need to correct the errors, which is often more time consuming than the seeding.

Cheers,
Richard

Thank you very much for your quick reply! I’m excited to try this out!

Best,
Minya