Wildtype flies and flight simulator Part 2

on Monday, June 11th, 2018 1:29 | by

Replicated wild type berlin flies in the flight simulator

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Wildtype flies and flight simulator

on Monday, June 4th, 2018 9:18 | by

The results from wiltype Berlin flies in the flight simulator.

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EMD with ICA to one sample of torque trace

on Monday, March 19th, 2018 2:35 | by

Trace segment from Maye et al. 2007 in the uniform arena

 

Trace after filtering by selecting the first 8 IMFs (intrinsic mode functions) from EMD (empirical mode decomposition). Since the signal should be quite clean I do not take out the first IMFs. The last IMFs, however, are too slow and change the baseline to much

Some examples of the IMFs obtained from EMD:

Since this is separating behavior adapting to the data intrinsic time scales I am now thinking of analysing with the SMAP algorithm to see if the behavior is more or less nonlinear at certain time scales.

In addition, I have thought of using ICA (Independent component analysis), that is an algorithm famous for the blind source separation problem by extracting the most independent signals from the input signals (in this case the IMFs which are different time scales of the behavior). So the ICs should consist of mixes of different time scales that are correlated together and thus belong (but not necessarily) to the same action/movement module/… Here a few ICs (from 10). My idea is that muscles might coordinate independently between ICs but coordinated within ICs. However to prove that is not that easy I guess

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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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Droso Kurs and more

on Friday, April 22nd, 2016 6:18 | by

praktikumandmine

Here I attach the results in a pdf file from the students praktikum with an additional line I tested on my own meanwhile (Gr28bd and TrpA1 drivers together). They seem to work as a really good positive control btw, good for technique optimization.

For the students I tried out two different split drivers, the MB058B, which targets PPL1-a’2a2, and MB301B, which targets PAM-b2b’2. In addition the Gr5a driver, because it targets the “sugar” neurons. From the split drivers I wanted to see if I still get a validation from my initial model. MB301B seems to do quite what my model would predict but MB058B maybe not. Hopefully in a future screen I would be able to test many more and make a much more precise modelling.valences

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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).

Correl-startingzero-c105>TNTfirstpredCorrel-norm-c105>TNTfirstpred

RMSE-startingzero-c105>TNTfirstpredRMSE-norm-c105>TNTfirstpred

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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.

c105;;c232>TNT:

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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Modelling the T-maze screen

linearmodelling

 

This is the markdown showing the protocol and results of the modelling for the choice in the T-maze. This is for calculating valence. Nevertheless, this needs to be confirmed with the results of more lines, it could be that it is overfitted, I would like to do in addition cross-validation. I´m actually doing crosses and finding new lines to have more lines to test.

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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.

 

 

platformc105xtntCorrelation

platformc105xtntRMSE

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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