More on the attractor

on Monday, October 16th, 2017 2:26 | by

Video of the attractor projected from a chunk of flight trace. Here one can see the difference in the trajectories of up- and down spikes. So here is another way of spike sorting by the way :).



Coloured traces depending where the locate in the attractor projection. Green means that they lie outside and when they stay with the PCs around zero its in red. The fly1r above does not look so clean as the v8 fly below (the cleanest measure I have)

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SMAP results

on Monday, October 9th, 2017 2:34 | by

These are the results of the SMAP for the TNTxWTB. I also have done a few for the c105;;c232xWTB but there is not much to say. I would say that the cleanest lines show a bigger slope, but prone to subjectiveness.

In addition, I have done some animations of the attractors that I have posted on slack because of size.

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Attractors for c105;;c232>TNT

on Monday, October 2nd, 2017 5:35 | by


This is what I showed about one fly from this line showing the attractor.

This graph is what I forgot to show in the lab meeting. There are the 6 best traces from this same line. All of them selected ad hoc subjectively. The three best of them to my eyes are exactly the three above in the graph (v8-this one is the one shown in the picture with the attractors-,v4,v2). What does this means? the ones with better traces (subjectively) have higher offset in the phi, this means that they are more predictable overall (maybe because more resolution?). In addition, they show higher slopes which means more nonlinearity.


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Drosophila behavioural flexibility towards food (3)

on Saturday, February 11th, 2017 10:21 | by

This time I tried to induce a kind of Garcia effect (eating something, feeling sick and then avoiding eating that again) in Drosophila. As one can see in the video below, Drosophila show inhibited proboscis extension response (PER) right after the onset of the US (intestinal discomfort).


However, the conditioned response is extinguished after several hours. I tried to use groups of 20 starved flies on yeast+water for 2h, food + 0.1% hydrogen peroxyde for 1h, starving with nothing for 1h (always inside vials), and then testing with conditioned food against another food for 2h (inside Petri dishes). It didn’t work: in the end they show the same preference as controls (without hydrogen peroxyde). I tried to condition sucrose, glycine, pineapple juice (and then test against apple juice) and nothing, the flies avoid at first but once the swelling goes away, they forget or don’t associate anything bad or sufficiently bad with that food anymore, and continue to prefer it.

I also confirmed the PER suppression following conditioning with quinine reported in [C. Keene A, Masek P. Optogenetic Induction of Aversive Taste Memory. Neuroscience. 2012;222:173-180]. However, it is also extinguished minutes (~30) after the conditioning, as their results also show (in my case, I used sucrose instead of fructose):

(my results:)

(their results:)

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Drosophila behavioural flexibility towards food (2)

on Thursday, February 2nd, 2017 9:49 | by

This time I tested how the behaviour changes with the proportion between the positive stimulus (sucrose) and the negative stimulus (quinine) and how it changes with the presence of a positive odour (vinegar) or a negative odour (benzaldehyde).

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Drosophila behavioural flexibility towards food

on Saturday, January 28th, 2017 12:05 | by

Why does one choose a burger over a carrot? How much is it possible to change that choice? What can Drosophila tell us about it?

I wanted to study Drosophila spontaneous behaviour regarding their food preferences and how malleable it is, so I can then try to condition it – and one should notice that those are “preferences” and therefore not neutral CS to begin with, as usual.
For that I used wild type Drosophila starved for 24 hours.
Drosophila likes the sweetness and the nutritional value of sucrose and does not like the bitter taste of quinine. Vinegar is a well-known attractant and benzaldehyde a well-known repellent.
To test the food preferences I simply add different food colouring to the food, test the flies in Petri dishes with alternated 10µL food drops and then, after 2h at 25°C and without light, I freeze them and count the number of flies based on the colour of their abdomen:


Here I present my first results:

(n = number of trials, each using 40 flies.)



As an illustration, here I have a short video showing a few flies during their initial food exposure:

And here the results with food in the presence of odours:

(The odours were placed in a small piece of filter paper inside the Petri dish.)


Next I would like to see if I can change their preferences (using these foods or sucrose vs fructose, etc.) through conditioning (as in the Garcia effect). Suggestions are welcomed.

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Cumulative bins, starting at zero and normalizing

on Monday, April 4th, 2016 3:04 | by

In the last meeting Björn proposed to do correlations of cumulative increasing bins. He said to do that taking the zeroth point (last library point where prediction is still not done) and use it for having a potential 1 of correlation coefficient at the beginning. I could not do that because I didnt save the zeroth points, and this will be a bit tedious and confusing considering that many flies were tested and probably the order is not 100% known. Thus, I just did the bins skipping this zeroth point. After all, we should see something similar with this one. First two graphs: c105;;c232>TNT (first and second prediction point), second: WTBxTNT, third: WTBxc105;;c232.

c105>TNTcumbinsfirst predCorrelationbothneigh

c105>TNTcumbinssec predCorrelationbothneigh

WTBxTNTTNTxWTBcumbinsfirst predCorrelationbothneighTNTxWTBcumbinssec predCorrelationbothneigh

WTBxc105;;c232.WTBxc105first predCorrelationbothneighWTBxc105sec predCorrelationbothneigh


Examples of how each of the flies look like. So they are basically cumulative bins with each single fly (each in different colour). Just to have a hint how does the singularity looks like.  exampleallfliesb exampleallfliescumbins exampleallfliesr   Second thing I did is normalize the to have a range from -1 to 1 all of them (I have to double check the range in the script) and also setting them at a starting point of zero. I did this because we do not want to have differences in the correlation coefficient due to a different offset of the values of the wing beat and neither because of the starting point (if the fly was already flying to the right full gas, then it could be that it has an influence in the following prediction).

c105;;c232 –> first at starting at zero without normalizing and then with normalizing. The next is just the RMSE (not so important).



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Prediction with binnning

on Monday, March 21st, 2016 1:13 | by

To see if there is an exponential decay in the prediction of the fly traces we did correlations of bins of 40 data points. We have 4 graphs (the last one merged) which consist of predictions at two different points with two different number of neighbours used for the prediction. So we have for each group sucesively: prediction at the first prediction point with the first number of neigbours, then the same with different number of neighbours. The last two are two different numbers of neighbours for the second prediction point. In the order: c105;;c232>TNT, TNTxWTB, c105;;c232xWTBc105;;c232xTNTfirst predCorrelationfirstneighc105;;c232xTNTfirst predCorrelationsecondneighc105;;c232xTNTsec predCorrelationfirstneighc105;;c232xTNTsec predCorrelationsecondneighTNTxWTBfirst predCorrelationfirstneighTNTxWTBfirst predCorrelationsecondneighTNTxWTBsec predCorrelationfirstneighTNTxWTBsec predCorrelationsecondneighc105;;c232xWTBfirst predCorrelationbothneighc105;;c232xWTBsec predCorrelationbothneigh

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Nonlinear signature of Drosophila in Strokelitude

on Monday, March 14th, 2016 1:48 | by





This is now the results from trying to predict the fly behavior doing ensembles of two predictions for the next 200 data points at two different points of the traces.


c105xTNT200Correlationdouble c105xTNT200RMSEdouble

WTBxTNT: tntxwtb200Correlationdouble tntxwtb200RMSEdouble

WTBxc105;;c232: wtbxc105200Correlationdouble wtbxc105200RMSEdouble

From what we see here, there is no “flattening” in the prediction of the fly when the neurons under c105 and c232 are targeted by TNT. This is  done with around 14/15 flies for each group with two predictions in each ensemble of the two starting points. That makes a total of 15flies x 3 groups x 2 starting points for prediction x 2 predictions per ensemble = 180 prediction traces. Now I´m trying to calculate it by making correlations of bins in the prediction-observed for the same fly

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Fly behavior prediction in the platform

on Monday, February 15th, 2016 2:25 | by

This is the prediction analysis of flies in the platform under a 20min experiment under dark conditions. The number of experiments change drastically among groups because of technical problems: WTBxTNT is 4, WTBxc105;;c232 is 22, for the experimental line is 6 (c105;;c232>TNT), for the platform without flies is 10. I show the root mean squares and the correlation coefficient for each group.


This is the experimental group: c105;;c232>TNT.





The group without flies on the platform. I expect here to get a very good predictability overall:

platformnothingCorrelation platformnothingRMSE


WTBxc105;;c232 groupplatformwtbxc105Correlation platformwtbxc105RMSEWTBxUAS-TNT platformwtbxtntCorrelation platformwtbxtntRMSE


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