Discuss introducing a new trace for background activity in SegmentationExtractor

[alessandratrapani]

What would you like to see added to ROI Extractors?

I would like to introduce two separate traces with their respective spatial components:

1. _roi_response_neuropil with the respective _neuropil_images_masks. This can be used to store the actual neuropil signals that sometimes refer to the area surrounding the ROIs.
2. _roi_response_background with the respective _background_images_masks. This can be used more generally to store the signal in the field of view that excludes the areas in the identified ROIs.

Right now we define the following:

roiextractors/src/roiextractors/segmentationextractor.py

Lines 34 to 47 in a6873d2

	def __init__(self):
	"""Create a new SegmentationExtractor for a specific data format (unique to each child SegmentationExtractor)."""
	self._sampling_frequency = None
	self._times = None
	self._channel_names = ["OpticalChannel"]
	self._num_planes = 1
	self._roi_response_raw = None
	self._roi_response_dff = None
	self._roi_response_neuropil = None
	self._roi_response_denoised = None
	self._roi_response_deconvolved = None
	self._image_correlation = None
	self._image_mean = None
	self._image_mask = None

Maybe I would also add one for baseline (_roi_response_baseline) activity which spatial components are in common with the _roi_response_raw, _roi_response_denoised, _roi_response_deconvolved etc..

And _image_maximum_projection to store the maximum projection image that is also a very common summary image for segmentation algos.

@pauladkisson, @h-mayorquin, @weiglszonja @ehennestad what do you think?

Do you have any interest in helping implement the feature?

Yes.

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[pauladkisson]

This is exactly the sort of API improvement that should be a part of roiextractors 0.6.0.

Just need to figure out how to make it work with our funding situation...

[h-mayorquin]

Now that we have merged #368, is minian one extractor where we can extract both traces? both neuropil and background? So we can keep this as a TODO.

Is there any other segmentation algorithm where this is possible.

[alessandratrapani]

Now that we have merged #368, is minian one extractor where we can extract both traces? both neuropil and background?

No, it only defines background.

[alessandratrapani]

Is there any other segmentation algorithm where this is possible?

I am not aware of a segmentation algorithm that outputs both, especially because the definition of neuropil is a bit controversial.
We could keep both to allow correct naming.

[h-mayorquin]

I have a proposal for this in #492