Thank you for your reply.
I was indeed, talking about the Gatetool yes.
As I mentioned, I managed to generate good binary images of my P. aeruginosa timelapses using Ilastik. I am measuring the production of a fluorescent component, and I have several strains with different production capacities in the mix. Let´s call them WT, A and B.
I have been able to obtain the distribution of the production for each of them in the mix and now we want to move to studies within the microcolonies.
I assumed that having a set of binary images would make tracking way easier for super segger in order to start generating lineage trees. I also tried oufti -recognises the first timesteps and then loses them- and Lineage mapper - is able so far to track for how long the cell is present, but no mother/daughter link-.
We still need to define what we want to do, but we find ourselves quite limited when it comes to software, as we are no experts at all.
For example, I have a WT producer and I want to see how daughter cells behave (production, growthrate,displacement…) when there are other cells A or B around, in the centre of the colonies or on the edges. Apart from that, there might be the circumstance that lineages stop, depending on specific combinations/densities of cells.
That´s why we thought the Gatetool would help us with the selection to focus on specifc cells.
If you have any ideas they will be more than welcome!