Refitting On_ACID results

[StoyoKaramihalev]

Morning! A huge thank you for this wonderful tool, it's been really fun to explore. And thank you for bringing into my life the results of a google search for "caiman on acid".

I've been testing out On_ACID with some 1P - new neurons pop up as the algorithm progresses over time, which is fine. But then can I refit the data with the final set of components? The ones that "appear" later in the recording (image below) are almost certainly already there in the beginning, so would be great to see what they were up to earlier.

Incidentally, I realise the offline approach might be better suited here, but the data and RAM overheads are pretty difficult to manage. Hundreds of GB of mmap files for short (and spatially downsampled) recordings mean I can only do this on a cluster with a lot of spare room.

Any help will be appreciated. Thanks!

[kushalkolar]

You should be able to pass in the spatial footprints you find a the end of OnACID-E to the OnACID constructor as Ain, see here:

CaImAn/caiman/source_extraction/cnmf/online_cnmf.py

Lines 99 to 101 in 9b0b79c

	Ain: csc_matrix, optional
	binary masked for seeded initialization as a Compressed Sparse Column matrix.
	To use set ``"init_method"`` to ``"seeded"``

I wonder what you would get if you gave it the existing model instead? I would try:

oncacid_obj # from previous run

onacid_iter2 = OnACID(params=same_params, Ain=onacid_obj.estimates.A)

# not entirely sure what this would do, Johanness would have a better answer
onacid_iter2 = OnACID(params=same_params, estimates=onacid_obj.estimates)

[StoyoKaramihalev]

Thanks a lot! Seems to have worked!

[kushalkolar]

It would be useful if you could let us know exactly what worked and what the components look like.

[StoyoKaramihalev]

The first option: onacid_iter2 = OnACID(params=same_params, Ain=onacid_obj.estimates.A). Followed by onacid_iter2.fit_online() - reran everything and returned an object with exactly the same components. I don't really know what goes on under the hood there, so can't say if it might've come back with some new components under other circumstances.