Discussion: meetings/2025-06-10

[jeromelecoq]

Please post your presentations here so that we can discuss in writing.

[lrudelt]

Hi everyone, how shall we proceed with the discussions of potential changes of the stimulus design (in response to feedback from preliminary analyses)?

Would you like to discuss these things here in the meeting discussion, or in a separate thread (e.g., #54)? Having a separate thread might make it easier to comprehend at a later point the rational that led to changes in the stimulus design.

[jeromelecoq]

I propose :
1/ we need to consolidate the analysis with control for bleaching. This is an important caveat that could influence what we derive from the existing data. We are about to share newer files with F0 that should help there. I have asked @rcpeene to prepare a notebook that we can share at the next meeting to demonstrate that first step.
2/ Everyone should include this controls in their analysis to make sure we rule out this confound.
3/ Once this has been done, I think we should include everyone latest results. I agree aggregating proposal changes in the separate thread makes sense. Feel free to start it if ti does exist. #54 could be a good start, although I am not sure the data we have shared can speak to the content of that thread, can it?

[lrudelt]

Agreed, including F0 would help a lot to refine the current analyses to with respect to the bleaching confound.

Regarding 3/ I also think that the current post is quite specific to this one proposal, I would include a more general post that invites everyone to post any caveats with the current stimulus design that they encountered during their analyses, as well us potential proposals. Would that make sense?

[lrudelt]

Contextual modulation of synaptic inputs during oddball

In this meeting, I would like to share some preliminary results on the analysis of the SLAP2 data. Please find the slides here.

Analysis code: https://colab.research.google.com/drive/1rbVXa0x8xn0Mz18ejZoc6Ald6f6R6dDq?usp=sharing
The code is based on code by @maierav, @jeromelecoq and @Sarruedi.
The analysis is related to the analysis by @Dedalus9 presented in #89 .

My focus was on investigating contextual modulation of synaptic inputs for expected versus unexpected sensory stimuli (e.g., similar to Hamm et al. 2021, or Furutachi et al., 2024 for somatic responses).
Thus, the idea was to do a similar analysis to panels I and J of Fig 1 in Hamm et al. 2021 (see below), but for individual ROIs, reflecting individual synapses.

Precise question addressed: Do we find evidence for the suppression of synaptic responses for expected inputs and enhancement for unexpected inputs? What is the spatial distribution of these responses (basal vs apical, or even branch specific?).

Preliminary results: Significant (average) modulation of synaptic inputs through stimulus context is quite rare, with few ROIs showing suppression of the standard stimulus, and very few ROIs showing enhancement of unexpected stimuli (45 and 90 degree orientation oddballs). Such modulations were mainly found in the 2025-05-08 experiment for image plain DMD1 (corresponding to synapses onto proximal dendrites). See slides for plots and more details.

Important caveats:

• The current stimulus design only allows to observe a given stimulus either as expected, or unexpected, respectively, which does not allow to study the relation between suppression and enhancement for the same stimulus (i.e., we miss one condition as in the plot by Hamm et al.).
• We are currently lacking controls for the static and contrast oddballs, so these have been omitted in the analysis.
• Due to photobleaching, we have to be careful in the interpretation of the current results. To mitigate this effect some extent, I split the data set in two halves, and compared the first half of oddball responses for each stimulus orientation to its control in the first direction selectivity block (previous to the oddball block), and the second half of the oddball block to the second direction selectivity block (immediately after the oddball block). This reduces the effect of bleaching between the compared conditions. Also, this way we can be quite certain that enhanced responses in the first oddball half, as well as suppressed responses in the second oddball half are not caused by bleaching.
• Statistical testing is still preliminary, e.g., proper multiple-comparison correction is not yet implemented

Figure from Hamm et al., PNAS 2021

[lrudelt]

Interesting example of changes in stimulus tuning after oddball block

This ROI is interesting, because there is quite an interesting tuning (on response to 90 and 45 degrees, off response to 0 and 45 degrees) appearing after the oddball block, thus only showing in the control condition of the second half of the recording (direction tuning block). This is most likely not a confound of bleaching, because the response should be weaker in the second control block.

[lrudelt]

Few significant modulated responses in DMD 2 or any imaging plane of the other data set

Few significant cases of suppression and enhancement in DMD 2 of the same data set as above. Especially, these could be confounds of bleaching.

Few significant cases of suppression and enhancement in DMD 1 of data set 2025-04-24.

Same for DMD 2...

[jeromelecoq]

Mean z-score differences between control and oddball for spatial ROI map

This is a spatial plot of the z-score difference between control and oddball conditions for DMD 1 in the 2025-05-08 data set.

#### Explanation * Circles are located at the coordinates of ROIs in the imaging plane * Circle size indicates the mean z-score over the entire recording half (including the orientation tuning and oddball condition) -> big circles indicate strong response to given stimulus * Color map indicates mean z-score difference between control and oddball condition for given stimulus direction (red indicates enhancement, blue indicates suppression)

Observations

• Consistent with bleaching, in the first half we find more suppression of oddball vs control responses across all stimulus directions (even the deviant ones), because in the first half the control block precedes the oddball block.
• In line with this, in the second half we find more enhancement of oddball vs control, because in the second half the oddball
  precedes the control block

How did you calculate the zscore here? Specifically over what is the STD calculated?

[lrudelt]

The mean and std for the z-score are taken over the entire recording half (including orientation tuning and oddball block). All trails of control and oddball (redundant/deviant) are thus z-scored with the same mean and std in the respective recording half, thus we are effectively comparing responses in Delta F here. The z-score just facilitates comparison between recording halves and different ROIs.

I personally find it easier to compare the oddball and control conditions like this. However, I do not have a lot of experience in analyzing ophys data, so really happy for any feedback and suggestions here!

[lrudelt]

BTW, I noticed that some replies are sometimes hidden by default, in the first reply to this post I put an example where the averaging, z-score etc is explained and it's easier to see how the analysis works.

[maierav]

ORIENTATION TUNING ANALYSIS

Code:
https://colab.research.google.com/drive/1bVMf9StUK4Vsh9b4BQj65vMiLlMtsBWi?usp=sharing

There were 2 blocks for orientation tuning (pre and post oddball)

Artifacts (spikes) in the timeseries can cause issues for arithmetic means (median helps)

Example ROI result

Polar plot as a superior visualization

pre vs. post analysis (no normalization yet!)

[hbelski]

Hi all,

I want to cement the agenda for this meeting:

So far @rcpeene and @lrudelt will present their SLAP 2 analysis (outlines above), If anyone else has another other analysis to present, please post is here so the group can review and our discussion can have context.

Thanks!

Hannah

[jeromelecoq]

Just to note, I am planning to present updates on stimulus development at the end.

[Sarruedi]

I can skip presenting analysis week next as I would like the analysis to integrate the bleaching correction. I hope we have sufficient time to talk about the stimulus development and discuss some issues raised by Lukas regarding the stimulus choices we made.

[jeromelecoq]

So tomorrow :
@rcpeene will start with an introduction on the newer traces with DF/F and F0.
@lrudelt will speak about his analysis introduced here.
@jeromelecoq will speak about current efforts to wrap bonsai with a python script to provide reproducible deployment and parameter tracking and control.