Questions on arboretum features

[pablooriol2]

Hi @quantumjot,

I was very excited to see this repo existing when browsing through the Bayesian Tracker repo!

I've just tried using btrack for the first time but I am having a hard time visualising the tracks. I've managed to do so in napari, but it's not that obvious (especially if you don't 'speak' the python language very well) and the fact that I would need to translate the tracks to my segmentation masks is beyond me at this moment in time.

So I was wondering when (more or less) would you expect to release a working plugin? Would it be as easy as feeding the plugin the 'tracks' variable generated from the tracker? What features would it have?

I understand that btrack is specifically designed for lineage tracing, and that the features of this plugin will align with that objective. It is not my current purpose though; I'm just interested in good cell tracking. Therefore, there are other features that would be particularly useful for general tracking purposes.

A sort of a wish list I guess (in order of preference):

• a button/function that labels the original segmented masks with the track IDs
• view & edit (whole sequence) tracks such as in TrackMate/TrackScheme or MaMut in ImageJ
• a slider that enables to filter tracks according to track duration
• being able to select tracks from the 'tracks' layer and have a view of the tracks along a whole time series
• a button/function that upon clicking updates tracks after user has amended them (unless this is done on the fly, as the user edits?)

These are features that would be really useful in my case (and I would guess for many other people tracking cells over time). I just wanted to put it out there to 1) see which (if any) of these features are on the arboretum roadmap and 2) as a suggestion.

Looking forward to hearing from you and seeing this plugin come to life.

Cheers,

Pablo

[quantumjot]

I'm glad you're excited about this, and hope the tracker works well for your system. Thanks for the suggestions re: the plugin - these are really helpful. I'm adding most of these as default behaviour atm, except the track editing. Keep watching this repo, I'll be updating it over the next few weeks.

[quantumjot]

There is a simple working version available now. It's still a work in progress, but you can load your segmentation, localize the cells and track them directly from napari. There are no options to tweak the tracking atm. The localization step is a little slow also, but that can be sped that up.

[pablooriol2]

Sounds awesome! Will give a try and let you know