Alternatives to supersegger image cytometry?

Hi all,

I managed to process several time lapses of P. aeruginosa with Ilastik and ImageJ, obtaining the ROIs perfectly matching my cells.

When it comes to analyzing the data, I always found supersegger interesting, as it offers the posibility to work in similar ways to flow cytometry.

The problem is that I do not know how (if possible) to feed the data from Ilastik and ImageJ to supersegger (I tried to generate ROIs in super segger using binaries from Ilastik and did not work).

So, is there any tool similar to supersegger that can be fed with pre-segmented data, allowing to basically use a virtual cytometer?

Thank you very much

I don’t think a lot of members of this forum are familiar with SuperSegger (it was new to me at least…), so I’m linking to the project page here:

If I understand correctly, you’re referring to the GateTool (see tutorial) here?

They seem to use their custom format of nested MATLAB structs to store cell (segmentation) data, so I guess it’ll be difficult to convert your ImageJ/Ilastik segmentations into that format without some scripting.

For what it’s worth, I invited Paul Wiggins, the maintainer of SuperSegger, to join this topic.


Would you be able to be a bit more specific, and describe the kind of analysis you’d like to achieve? Maybe you can upload a few example figures to illustrate what you mean? I’m sure this will make it easier for others to help you.

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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!