Interpolations and Spike analysis

on Monday, December 7th, 2015 2:42 | by

rawplot markeddeleted splineThis is just a proof of concept how useful the interpolation is for this purpose: and I would say it´s almost useless. If I delete from the raw data (1st graph) some pieces (2nd graph), and I make a spline interpolation (3rd graph) it doesn´t match that well. Linear interpolation was done in previous weeks with not much of a success. Anyway, the result of a linear interpolation can be imagined by eye just by joinning the two ends with a straight line, and this doesn´t occur in the fly behavior as we can see in the raw data (1st graph).

Ute spike1openloop1 spikesannotatedints spikesdatavsmyspikesThere could be two posibilities for spike detection: one is the one from Ute and the other one is the one from Maye. It seems to me that the one from Maye is more precise. I have run the script but I do not get so many spike detections as he gets. I did try several thresholds for spike detection and doesn´t change very much. So I have to work more on it to see what is really the important factor for a proper spike detection

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Measuring Wingstroke Amplitude with Strokelitude (III)

on Monday, November 23rd, 2015 2:59 | by

After the measurements of this week, I get better results in the trace of the fly;



With the corresponding trace exerpt with the spikes of the figure above (1)



and two more from other flies:

TraceDownsampledExceerpt TraceDownsampledExcerpt


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Measuring Wingstroke Amplitude with Strokelitude (II)

on Monday, November 16th, 2015 2:52 | by

After the results in tracing of the flies from last wee. This week I’ve improved detection of the wings and the care of the flies. The results seem similar to the flight of a fly. Attached we find the trace Downsampled of the best four flies I got:

TraceDownsampled TraceDownsampled TraceDownsampledTraceDownsampled

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Linear interpolation for solving uneven sampling in the platform

on Monday, November 16th, 2015 2:50 | by

PredictionTWOThis is the prediction of one of the controls (UAS-TNTxWTB) after being interpolated for compensating for the uneven sampling. The y-axis is Correlation coeficient (taking correlation of bins of 100 sampled points) for the next 2000 sampled points (x-axis). There seems to be no decay in the prediction, as if it was a random behavior. Aparently linear interpolation is not suited for this case. I have heard that linear interpolation is fine when sampling rate variation is low (like 5%). For this case, spline interpolation might be better. If this is really worth to do I don´t know, the best case would be for sure to have the hardware to sample according to the necessities.

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Spontaneity: Measuring Wingstroke Amplitude with Strokelitude

on Monday, November 9th, 2015 3:38 | by

Those are the results of measuring the wingstroke amplitude with Strokelitude and “The ping pong ball machine”. And analysed with R studio and the scripts written by an student.

The results are not too good, comparing them with the result obtained in other experiments.

Two pictures of the trace down-sampled of my flies:



and in the next picture is how it should be plotted:


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Sampling rate in the platform: looking for even sampling times

on Monday, September 28th, 2015 2:28 | by

withoutinternet2 SamplingrateHomogeneity of the sampling rate in the platform: is improved mainly by stopping any other running programs and the internet, setting priority in the CPU doesn´t improve much. This doesn´t completely solve the problem so the priority was also changed in the code of the software itself and the sampling frequency has been changed to a higher one (because this one isn´t enough for intrapolation from what I have seen) in order to be able to make intrapolation. However we will try to change this to around 62ms sampling because the system somehow tends to measure a this time. In addition I did model several behaviors (white noise random, oscilatory activity with three frequencies, and several chaotic systems: logistic, clifford and lorentz) to see what their parameters and graphs look like, but they all have very incongruent results, so it didn´t bring much info. I have to check if I´m setting the right values for the analysis parameters.

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Analysis for spontaneity in platform

on Monday, September 21st, 2015 2:26 | by

Samplingrate   RplotThe sampling rate is not homogeneous and this affect a lot the processing of the data for non linearity. What can be done? On the right we see a recurrent plot of one single fly in darkness for 5 min. It seems to be to some extent periodic, not much chaotic (but I need more experience to really guess that) For more information

In the table below we see a low recurrence but high determinism among many other parameters.





detrended fluctuation analysisThe E2 line shows values around 1 the whole time when the sample is random. This is contradicting the above. The detrended fluctuation analysis show a value around 0.5, which means that if these data was modelled as random it would look like white noise.

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publishing torque meters comparison

on Wednesday, March 6th, 2013 11:17 | by

here is the draft:

Is there any good publication describing the wing beat analyser?
other remarks?

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Trajectory data: database structure

on Thursday, December 20th, 2012 5:16 | by

CeTrAn is our software to analyse trajectory data, written in R it is free and open source . It was designed to analyse data obtained in the Buridan’s experiment setup. I am now trying to have a larger scope and incorporate different type of data:, for instance:

– Buridan’s experiment done with a different tracker

– Walking honeybee tracking in a rectangular arena, with a rewarded target

– Animal (flies/bees) walking on a ball, using open- or closed-loop experiment setup

– trajectory data obtained from the pysolo software (flies)

– larval crawling data

I want to include an automatic depository of the data in a database. Automatic entries in Figshare is for instance possible. (see older posts). My problem is to find a way to treat the data such that:

1. the raw data is uploaded

2. all data is uploaded also if we use only the centroid displacement (in some data file the head position is also given)

3. the data can be reused and data obtained in different lab, animal, setup can be compared. (data should be organized such that it can be searched and queried).

4. probably other elements that I do not think of….


My main problem: I have nearly no experience in data management/design, ontology or semantic web. Here is a first draft of a database structure that I have thought of. Every feedback would be welcome:

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C105-Gal4 S-Map results

on Wednesday, December 5th, 2012 5:49 | by

Here I post the S-Map results of the C105 gal4 lines crossed with TNT. Its part of the double line c105-c232 Gal4 that showed phenotype. Seems tetanus has some effect. C105-C232 Gal4 slope range was around 0.005.

N –  34, 37, 29 respectively

Rest of the analysis on the way !


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