Christian Rohrsen

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Mean trace of all flies and how degrees of freedom vary over learning

on Monday, July 23rd, 2018 6:40

Mean trace of the positive control in the Joystick to get to see what are the overall dynamics and maybe to get an idea what might be the best score to pick.Here the standard deviation of the flies along the time axis. This is just to see if all the flies have more similar phenotypes with each other or not at each time.

This is to see if the flies have less degrees of freedom at any segment by measuring the standard deviation at each segment. There does not seem to be any effect. Although this might be mixed with the wiggle scores. I think measuring entropy is a better measure.

 

All the same plots as above but for TH-D’, the interesting line from the screen.

 

Standard deviation across flies

Standard deviation across segments

Performance index for modelling for data in the Y-mazes

on

This are the performance indices for the different models performed to estimate the valence of the dopaminergic clusters. AIC: Akaike Information Criteria; BIC: Bayesian information Criteria; LogLikelihood: log Likelihood estimation

lm: linear model

+ int: taking double interaccions into consideration

b lm: bayesian linear model with bayesglm function

b lm MCMC: bayesian linear model with MCMCglm function

nlm: nonlinear model with lm function with splines fitted

b nlm: splines fitted to each cluster and MCMCglm function

GAM: general additive model with gam function

 

Adding double interactions seems to produce better models, nonlinearities also make models better and frequentist also. To me it seems like this  data might be noise and therefore adding interactions, nonlinearities and frequentist methods is just fitting the noise better (overfitting) and that is why I get better scores with them. In addition, care needs to be taken since I use different functions that calculate the model performance scores differently (although the formulas are theoretically the same for all!)

Finding the interesting lines

on Friday, July 20th, 2018 3:46

This is the correlation from the T-maze experiments from Gaia and Naman. Neither ranked nor regular correlation show any significant effect. This means that these effects seem to be random, at least for most of them, is this an overfitting result?

I would say blue 1 is a line that was negative for all the tests I have so far seen. So this might be an interesting line. What to do next?

I would unblind the blue1, which is TH-D’. It was shown to be required for classical conditionning in shock and temperature learning (Galili et al. 2014). Another interesting observation is that th-g4+th-g80 seems to have like zero PI scores in all of the experiments (Naman and Gaia in the Tmaze, Joystick and Y-mazes). So could it be that all of these neurons have indeed a meaning, but is depending every time in the context?? Maybe Vanessa Ruta´s work might be interesting for that.

More on valence inference

on Monday, July 2nd, 2018 2:00

This is the linear model with its statistics

 

This is the linear model adding interactions. It is perfectly possible to have interactions between neurons, kind of what occurs with olfactory processing where ORNs activated alone or in different combinations have completely different meanings

 

 

I uploaded in slack the bayesian linear model with interactions. For any reason, it does not let me upload it now to the website

I am trying one of the ways of nonlinear models: GAM (Generalized additive models). Here one fit splines to the effects to certain degrees of freedom.

 

 

This is the kind of bar graphs I thought I could use for all the plots.

Modelling the valence of dopaminergic clusters from the Y-mazes

on Monday, June 25th, 2018 1:52

Dopaminergic clusters are differently targeted by the different Gal4s. Some of the express faintly, others stronger. Here I try to see if the dose-response curve (or expression-PI curve) seems to be linear or not. Here I put two examples from the 17 clusters, where the first two seem to have nonlinear curves, with and optimal expression level, and the last two seem to have a linear response curve.

This will be important for the modelling in order to decide to make a linear/nonlinear model. Down below I show the results from a linear model and it´s statistics. From Aso et al. 2012, one could see that activating the lines with TrpA1 shows a linear response curve. But in this case it does not necessarily seem to be the case. Therefore, light intensities might have an effect, as well as the expression level, and conclusion needs to be taken carefully.

 

In addition it is difficult to calculate this for all the clusters with just one single light intensity test, because not all clusters are expressed in several Gal4s to different level, so that we can estimate from there. So for the interesting lines we might need to make several experiments at different intensities, and see the dose response curve.

 

The G4s I have used for the modelling are the ones shown here.

Making new ratios for Y-maze

on Monday, June 18th, 2018 1:55

This is just to show that I am trying to find  a new ratio so that all graphs have from -1 to +1 ranges. That is why now the difference in occupancy time is divided by the total time. The same with the speed. Because speed differences are so subtle, the Y axis scale has to be lower

Sathish scripts in my hands are reproducing results

on Friday, May 18th, 2018 3:34

 

 

This is a picture of the supplemental figure from Maye et al. 2007

 

Below the results from the sathish scripts running on the data from Maye et al. 2007. It matches, so Sathish scripts in my hands work fine

Confocal images and boxplots from my results in strokelitude

on Tuesday, May 15th, 2018 12:26

Confocal image MAX stack of one of the brains at 20x

 

 

and at 40x

 

In this link we have a video of a 3D stainning pattern          zoomed_CC

 

In addition I add here teh boxplots from the final results of the Ping Pong ball setup with these experiments

Stainning c105;;c232

on Monday, May 14th, 2018 11:22

 

The first figure shows each of the central complex ring neurons types (Martín Pena et al., 2014). The c105-G4 targets the R1 neurons and the c232-G4 targets the R2 and the R4d neurons

This is the c105-G4 stainning from Martín Pena et al., 2014

232-G4 stainning from Kahsai et al., 2012

 

Axel stainning from c232-G4 alone

Axel stainning from c105-G4 alone

Axel stainning from both drivers together. I would say it really contains both driver lines.

This are both driver lines together as well from Axel. To me it seems that only c105 is present

This are my stainnings at the fluorescence microscope (no confocal). This is to show that in all of the 10-12 brains I have looked at, they all had the c232 pattern present

In addition, they had many more neurons outside from the central complex which I believe belong to the c105-G4 line. This is my only proof to show that c105 is also present, since the R1 neurons seem to be hidden when R2 neurons are stained.

I was also looking to the youtube video you have online, Björn. To me it seems I can only see the R1 ring neuron from the c105

Nonlinearity is present the fast timescales

on Wednesday, April 4th, 2018 3:38

After performing EMD to 6 fly traces of 20000 data points (that is 1000 sec flight) for each group (tntXwtb; c105;c232>tnt; c105;c232Xwtb). This data size was chosen to reduce computing time of the SMAP procedure. The EMD decomposes the trace into different time scales in nonstationary data. It seems that the nonlinear behavior occurs at the first IMF (the fastest time scale) and a bit in the second IMF. The potential conclusion to this is that the behavior of the the fly is only unpredictable at the fast movements whereas slow movements are very predictable. Nevertheless, to be cautious it could be that this fastest timescale is just noise, and that this noise is nonlinear. I would say that there is no difference at any time scale between groups (pay attention to the different ranges in the Y-axes), so the ring neurons R1, R3, R4d do not have any effect.

As a groundtruth I have used the same analysis pipeline for the traces in the uniform arena from Maye et al. 2007. Here the effect is even more pronounced at the fastest time scales. So I will conclude that this is real fly behavior and not noise that is shared among both setups: the Ping pong ball machine and the torquemeter.In order to gain more insights into the underlying flight structure I took one random flight trace to explain a few observations. The x-axis is the theta (that actually goes from 0-4 in steps of 0.2 and therefore we see the 21 points), in the y-axis is the correlation of the prediction to groundtruth. We see that IMF has a bigger slope, but not only that, also that its prediction correlation is around 0.88, whereas lower timescales prediction is basically perfect. That is, fast time scales are not only more nonlinear but also less unpredictable. This pattern is repeated in every fly measured

 

To have an impression of how these IMF resultant traces look like: IMF1, IMF2 and IMF8