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Relevant features of holographic stimulus #1
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@alessandratrapani Thank you for working on this!
Example output from xml for reference:
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For @weiglszonja how do we communicate the spiral activation pattern the laser takes? Is that also typical of the Adesnik data? |
There is no spiral activation pattern in Adesnik data. They target the whole ROI volume at once (in ScanImage coordinates) where they expect to be cell bodies. |
Sorry for taking so long but I wanted to have a clearer picture. Here are some basic notes I gathered from different papers, (most of the notes are from the one suggested by Pinto lab for the methodology they used). Critical features for holographic optogenetic stimulationEffector (opsin, membrane channel): (equivalent of Indicator for imaging)
Laser: (Device)
Beam pattern (on single cells): (probably it should go in the equivalent
temporal focusing: (as in Abdeladim, Lamiae, et al. "Probing inter-areal computations with a cellular resolution two-photon holographic mesoscope." bioRxiv (2023): 2023-03.)
ROI excitation (equivalent of ROIresponse for imaging)
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@alessandratrapani Thank you for collecting these features!
tool mentioned in the article for photoactivation response mapping: |
I thought this too, I just don't know if we have the actual TimeSeries for the stimulus to each ROI |
How can we deal with different stimulus patterns with different descriptive parameters? |
How about having "base" |
I'm compiling the MarkPoints.xml files to collect the times based on Neto's description
This was my understanding but could be wrong. |
This looks like it's really starting to come together! Very cool to finally be able to dig into specific details of how this method works...
As discussed from our meeting; I highly recommend avoiding having multiple attributes that are interrelated functionally - in this case 'average power' being a function of other attributes - meaning it's possible for someone to input inconsistent values across the neurodata object (BTW can you post a screenshot or copy/paste of that section of the paper you showed me to have it here for reference?) If it's unavoidable it means we'd which we then need special validators (Inspector checks) for it, but if there's a better design to be created here that can avoid that complexity, it would be preferred Also some of these attributes you mentioned being specific only to pulse lasers - if it's possible to condense this list down to more generic attributes that can apply to all laser types? Similar to the goal of the MicroscopySeries on the other extension? |
Maybe crazy idea for super generic representation of the stimulus patterns, since they have such diversity that text based metadata alone might never capture it; how about providing a 'summary image' of sorts that visually describes the excitation pattern? On the technological side we could have helper functions for retrieving the built-in types (all 4 of those from the paper figure) given a users string specification, but this would also enable them to specify anything customized in a way that is more explicit |
I think it can be feasible to describe the shape of the stimulus on the single ROIs, as in the case of the spiral pattern, but if the shape of the stimulus varies in time for the single ROI or it's different for each ROI, I think it scales up to a level of complexity that it's not necessary in the NWB representation. We don't report all the parameters in the preprocessing algorithms, as well as all the details in the surgical procedures, and I think this is on the same level since it's the description of the experimental protocol. Do you agree?
After reasoning on this I think that the way to go is to report only the laser power as a time series (like in the ogen module) for each targeted ROIs, similar to the ROIresponse container, but instead of the indicator we would have the effector and the default unit would be W. Does it make sense to you? |
I would like to propose this new structure in light of the new considerations:The new parameters added are marked in bold
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@alessandratrapani this looks great! For |
Oh yeah, sorry for the confusion. I meant the base should be |
@alessandratrapani Looks really good! Thank you for putting all of this together. I have a few questions/notes:
I know this is an inherited problem from ImagingPlane but the indicator could be calcium, voltage, neurotransmitter, etc. right? So I think we should be a bit less specific to allow more flexibility. Ex.
Similarly with effector I think we should use more inclusive language like
I disagree -- the precise spatiotemporal stimulus pattern could be a very important piece of data for any type of re-analysis of holographic optogenetic stimulation experiments. What if they stimulate the axon of a pre-synaptic neuron and then the dendrites of the post-synaptic neuron? Or vice versa? Importantly, as you pointed out, there are a variety of different stimulation patterns that one could use, and they grow complex as you scale the number of ROIs and sequential rounds of stim. I think it is reasonable to expect that as this technology matures, scientists and engineers will continue to explore different patterns of stimulation and flesh out the space of possibilities. With that in mind, I think it might be more appropriate to model the |
Yes, thank you for the suggestion! "Opsin or channel membrane" was already general enough for me, but I surely have a bias on these things. I like your description more. |
I generally agree with you, the best way to describe the stimulus pattern is to recreate the hologram, i.e. a 4D image. Nevertheless, since I don't have a strong position with this, I am open to any type of implementation, and maybe we can consult directly the point person for the holographic data in the Pinto lab and in the Adesnik lab. What do you think? |
Agree. I think you've really exposed the core issue here, which is a tension between designing for the very simple stimulus patterns for which we have examples (spiral from Pinto and whole ROI from Adesnik) vs. designing for the much more complex stimulus patterns that might arise in the future. Although I usually prefer to design with concrete examples in mind, I think we have an opportunity here to encourage good data practices by suggesting/requiring labs to provide the original stimulus hologram. It's important to remember that NWB isn't just a way to store data but also essentially a recommendation of what kinds of data/metadata are important to keep track of. This notion is really reinforced by perspective on neuroscience data standardization with NeurodataWithoutBorders Section 4.13. An indirect benefit of using NWB is improved data awareness. That being said, of course it's a big problem if labs don't have their stimulus hologram recorded and no easy way of reconstructing it. So, let's ask the Adesnik lab tomorrow and Pinto lab (somehow) and see what they think about all this and what kind of data they actually have. |
Very good point! I am quite sure that for Adesnik lab they would have the original stimulus hologram since the scope of the work is mainly to propose a new type of technology. |
I am reporting here some consideration from Professor Pinto: 4D-hologram is more complete, but it comes with a few non-straightforward decisions: a. The resolution:
b. Holographic patterns:
c. Stimulus parameter setting:
In their Datajoint pipeline they used a similar approach as we proposed in solution 2: Store a time series for the stimulus power delivered for each ROI plus a description of the type of stimulus.
In light of these considerations, I suggest staying within option 2 and additionally storing the SLM mask (if it is something we can actually request) along with the description. What do you all think? I will iterate again on this once we have the opinion from Adesnik lab. |
This is the real problematic one imo. Although I am a little bit confused how they can easily access the stim pattern per ROI in the imaging space but can't access it in the larger FOV. It should be the same time series just localized to an ROI right? I guess what they recorded are the commanded stim patterns rather than the measured stim patterns? If so that should be fine, but it might be nice to clarify in the docs/names. |
Seems like we should try to make 2 work for both stimulus patterns, with 5 as a fallback. |
I think we should keep the time series representation since it's more general. Although both labs that we're working with right now use fixed laser power per ROI, there is nothing technical preventing them from using continuously varying laser power (I think). Since it is easy to transform time intervals into a time series but hard to do with the reverse, I think we should stick with timeseries. |
Thank a lot for the feedbacks @pauladkisson |
While testing the extension, we realized we could not add a dynamic table or a generic NWBcontainer to the stimulus module. |
@weiglszonja Also had a good idea about how to create a general group without overriding the |
Yeah, so the idea is to add a new container that extends LabMetaData, which is an For reference this is how ndx-photometry does it https://github.com/catalystneuro/ndx-photometry/blob/7ea9d755ceac9524125f50ab528b403b135c4530/src/spec/create_extension_spec.py#L333 |
I would like to propose a change for the name of the extension. Instead of holographic-stimulation I think it's better to call it with a more generic denomination for patterned optogenetic stimulation:
What do you think about it? |
I don't have a strong opinion about this, if you feel this extension should be more general we can go with Would you also change the neurodata types as well? Or Holographic* would be a "sub" type of patterned stimulation? |
I also wanted to mention here https://github.com/bendichter/ndx-optogenetics , maybe for Device it can be relevant here? |
Haven't both labs referred to what do as holographic? Or are you saying the neurodata types would still have holographic references, just the overall name of the extension would be generalized? Normally I'd suggest keeping such an extension within a targeted scope specific to the new data we're modeling |
That is yet another extension for ogen, largely for trying to satisfy some particular users criticism of the lack of metadata surrounding the core ogen data types, but even that extension has been said by some to fall short (something about 'titer' parameters if I recall) and I would say if the Fiber Implant, etc aren't relevant to holographic specifically then they should be kept as their own extension just to keep the scope of our current needs manageable |
Yes, I just came across the issue. I think that there are some good reasonings that we should keep in mind:
The other observations are specific to optogenetic with fiber implants, but I also agree that you don't really need OptogeneticStimulusSite since location could be a property of the series directly as well as pattern in our case. That said I think it's better to keep it separate from our extension because that type of photostimulation is done with fiber implants, ours with 2p microscope (the same way fiber photometry is different from two photon imaging). All of these consideration might be good for a proposal for modifying the core ogen, right? |
Yes, over a longer time scale once each module has stabilized in its own right |
I would like to discuss a new proposal for the extension that would include all the info we need for the holographic series and possibly tackle some of the issues related to the current optogenetic series.
Major changes:
I know we are moving a bit far from the current implementation of the ogen module, which might create confusion. But I will leave this proposal here anyway for future discussion. |
What exactly are you referring to here? Is there a paper that uses a stimulation pattern like this?
Makes sense to me. Remember, we also discussed excitation lambda being miss placed and miss named for imaging in ndx-microscopy. It might be reasonable to include optogenetics in that NEP as well.
As pointed out in this issue, some metadata like the excitation lambda has been miss placed into the stimulus site instead of the stimulus series. As we discussed in ndx-microscopy, this problem also occurs with calcium imaging where meta-data is haphazardly thrown into the imaging plane object. However, I don't think that combining the stimulus site and stimulus series into one object is the appropriate solution. Instead, we should proceed as we did in ndx-microscopy: the stimulus site / imaging plane should be limited to only describe properties native to the actual site ex. location, effector/indicator, etc. Then, the other metadata can be moved either to the series object directly or to a separate object(s) that is referenced by the series object (ex. Microscope/Optic Channel in ndx-microscopy). Specifically, I recommend that the holographic stimulus site object has a location, effector, and rois. The holographic series object would have a device, stimulus pattern, site, and excitation wavelength. I also don't think we really need to specify the stimulation type, since effectors can have more diverse actions then just excitation or inhibition -- see this paper on using light-activated effector proteins for triggering intracellular signaling. I think it's better to just specify the effector by name, and then people can go look up what it does. |
Nice review paper here gave me the idea of calling it ndx-patterned-ogen
I like this solution, and I also thought about it, but since the series dimensions are n_times x n_rois I thought it would be best to have rois directly in the series object. However, if you think it is not a problem, I am happy to change in favor of this solution.
Except for changing the name from excitation wavelength to stimulation wavelength, right?
Thanks for the suggestion. I wasn't quite sure whether to include this or not, because I think it's an intrinsic feature of the effector. I will remove it. |
Thank you for the paper recommendation it was very informative, especially the summary table at the end. I agree that it is reasonable to incorporate non-holographic patterning methods into this extension such as 2 photon galvanometric mirror and auto acoustic deflectors –patterned optogenetics seems like a good name to me.
We do need to be careful about this one. What if one wanted to deliver stimulation to a subset of the total number of our rOIs for a given holographic series? Would you need to add zero for all of the ROIS that you're not stimulating in this particular series?
Yeah, just a typo on my part. |
Yes, exactly. Or you can always create an roi table that indexes only the stimulated rois. |
@weiglszonja @pauladkisson @CodyCBakerPhD
This first issue is just to collect notes on relevant features that should be included in the new neurodata type for HolographicSeries
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