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Link neuronal population (V2A) to ephys and behavior --POC-- #213

Open neuroBazzi opened 2 years ago

neuroBazzi commented 2 years ago

New request by the user for the NIH meeting

the concept is to link one neuronal population to other data types, electrophysiology and behavior. The concept is that the user right clicks on any one neuron of one population (V2A) and a drop down menu appears with two options 1) see electrophysiological data; 2) see behavioural data. The user click on either one of them, and the tab on the right (where the 2D viewer is) opens either on the corresponding tab (either electrophysiology (this one already exists) or Behavioural data (this one needs to be created)) and shows the content. At this time the content will be a PDF (coming from the client soon).

cc @zsinnema

neuroBazzi commented 2 years ago

Electrophysiological properties of V2a interneurons in the lumbar spinal cord.pdf Eohys table

afonsobspinto commented 2 years ago

@neuroBazzi

@afonsobspinto check this later: https://projects.wojtekmaj.pl/react-pdf/

neuroBazzi commented 2 years ago

@afonsobspinto

neuroBazzi commented 2 years ago

There will be a similar PDF coming for the behavioral tab but you can use the one of the ephys as placeholder if you need to work on it before they send us the behavioral PDF

afonsobspinto commented 2 years ago

@neuroBazzi

I think having in the 2D will be much much harder. Because the 2D viewer is just an image. There's no easy way to interact with it. For the 3D viewer the process is way simpler.

Is the PDF linked with the specific neuron clicked or just the population. In other words, if I have neuron A and neuron B of V2A population, will we show the same pdf if I click on A or B?

neuroBazzi commented 2 years ago

oh ok, sure, I was assuming the opposite so let's do it for the 3D only. I just spoke to them again, they're asking for a third tab (I don't think it makes much difference at this point). Same rules as the other two (click on the item in the dropdown and it opens a tab). The tab is called I/O Mapping and it'll contain another PDF (to come).

In all these cases, the PDF will be link to all the neurons of the population, it doesn't matter which one you click the action will be the same, all the neurons of the given population will be clickable and it will take to the same PDF. The mapping between populations and PDF is: 1) population V2 --> ephys PDF; 2) population V2 --> behaviour PDF (we don't have it yet) 3) population V1 (Steve will produce it over the WE) --> I/O mapping PDF (we don't have it yet)

I will create my own account and load the necessary populations. This is POC so you can hardcode things if you want to make things simpler

afonsobspinto commented 2 years ago
neuroBazzi commented 2 years ago

The population name is V1 or V2, we load them from a file that is named V1 or 2 (or V3 and so on), the name comes from that. PDFs are static, there is no V1 umbrella, there will be a population called V1 linked to one PDF (inside the PDF nothing changes)

neuroBazzi commented 2 years ago

@afonsobspinto @zsinnema @tarelli Summary of the synch with Zoran and Matteo 1) the tab on left is going to be only one, called Details, which is going to contain an accordion with the three sections: Electrophysiology, Behaviour, and I/O Mapping. Every section of the accordion can open/collapse to show the information within; 2) there will be no drop down, the population will link with left-click straight to the Details tab and show the accordion with the three sections closed; 3) The content of each section will be an image of the PDF (I learnt PDF are hard to show so we can take a snapshot of the PDF and show it as png); 4) The mapping between populations and content remains (population V2 has ephys and behavior PDF, but no mapping, population V1 has I/O mapping but no ephys/behavior PDF) 5) if a population has no information linked, the section of the accordion will display a standard message (No data available);

Zoran please feel free to add if I overlooked something

afonsobspinto commented 2 years ago

The population name is V1 or V2, we load them from a file that is named V1 or 2 (or V3 and so on), the name comes from that. PDFs are static, there is no V1 umbrella, there will be a population called V1 linked to one PDF (inside the PDF nothing changes)

Is the name exactly V1 or V2 or does the name includes V1? For example 'V1 Sp8' would link to V1 PDF? (Attaching an example of populations for context) image

neuroBazzi commented 2 years ago

Includes V1

afonsobspinto commented 2 years ago

In that case, using the same example as above, I'm confused by your comment 'there is no V1 umbrella'. Shouldn't the V1 (red) population and V1 Sp8 (green) population link to the same V1 pdf file?

neuroBazzi commented 2 years ago

Good catch, yes

On Mon, Oct 10, 2022, 17:25 Afonso Pinto @.***> wrote:

In that case, using the same example as above, I'm confused by your comment 'there is no V1 umbrella'. Shouldn't the V1 (red) population and V1 Sp8 (green) population link to the same V1 pdf file?

— Reply to this email directly, view it on GitHub https://github.com/MetaCell/salk-interactive-atlas/issues/213#issuecomment-1273482103, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANYX5OD57A43Y7ERWSIEH63WCQYQFANCNFSM6AAAAAAQ7JVINA . You are receiving this because you were mentioned.Message ID: @.***>

afonsobspinto commented 2 years ago

Can we click directly on the details tab? If so, how do we decide which population data are we showing? I assume the last selected would be the best option but what if there was no population selected yet?

Additionally, I think it would be nice to have some sort of UI indication on the details to easily show which population data I'm viewing

tarelli commented 2 years ago

Showing a PDF will be less light/trivial than showing an image, probably not necessary?

On Fri, 7 Oct 2022 at 18:59, Afonso Pinto @.***> wrote:

  • What tell us if a population belongs to V2 or V1?
  • Are the PDF's static? In other words, if I have 2 populations under the V1 umbrella, lets say A and B, in normal circumstances, does the content of the pdf for population A differs from the content of the pdf for population B?

— Reply to this email directly, view it on GitHub https://github.com/MetaCell/salk-interactive-atlas/issues/213#issuecomment-1271831935, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAATZZ2RUX66CLON7S4JC23WCBJGDANCNFSM6AAAAAAQ7JVINA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Matteo Cantarelli

Chief Technology Officer MetaCell, LLC Web: metacell.us Mobile: +44 (0)74 47540306 E-mail: @.***

neuroBazzi commented 2 years ago

@afonsobspinto yes we can click and open the details tab. We could display a message 'no population selected', also yes if you can think of and poc a way to show the selected population name in the accordion it would be great.

afonsobspinto commented 2 years ago

Hmm, I'm not sure I'm convinced by the 'no population selected'

Showing a PDF will be less light/trivial than showing an image, probably not necessary? On Fri, 7 Oct 2022 at 18:59, Afonso Pinto @.> wrote: - What tell us if a population belongs to V2 or V1? - Are the PDF's static? In other words, if I have 2 populations under the V1 umbrella, lets say A and B, in normal circumstances, does the content of the pdf for population A differs from the content of the pdf for population B? — Reply to this email directly, view it on GitHub <#213 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAATZZ2RUX66CLON7S4JC23WCBJGDANCNFSM6AAAAAAQ7JVINA . You are receiving this because you are subscribed to this thread.Message ID: @.> -- Matteo Cantarelli Chief Technology Officer MetaCell, LLC Web: metacell.us Mobile: +44 (0)74 47540306 E-mail: @.***

Right now I started the POC with an image. Imo, it is slightly easier that way but I wouldn't say showing a PDF is a blocker.

neuroBazzi commented 2 years ago

Presynaptic Input Table for Metacell .pdf this is the table for the I/O mapping, this PDF would link to any neuron of any population

zsinnema commented 2 years ago

@afonsobspinto can upi have a look at this? thanks!

neuroBazzi commented 2 years ago

V2a IN Behavior.pdf Behavior PDF

@afonsobspinto