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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Behavioral bursts on Pysolo midline crossing

on Thursday, October 18th, 2012 6:46 | by

I used 400 min data of midline crossing activity in pysolo to do the bursty analysis. All codes are ready and the following are figures.


Figure legend:



3. Wtb-TNT

1. Weibull distribution : K=1 denotes poisson process and published fly shape distribution k=0.46±0.07sem
















2.Burstiness factor :

Poisson process would be 0, while B >0 is from drosophila, human activity etc.,

3.Memory parameter:  I am still gathering information about it.

A Sorribes, BG Armendariz, D Lopez-Pigozzi, C Murga, GG de Polavieja   ‘The Origin of Behavioral Bursts in Decision-Making Circuitry’. PLoS Comp. Biol. 7(6): e1002075 (2011)


By the way , Is there a functionality to insert  .fig file and tiff file? I get empty image after uploading .tiff file.

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Category: Pysolo | 2 Comments

grip analysis on Buridan activity data

on Wednesday, October 17th, 2012 7:49 | by

Grip analysis on:

1. Interval between activities (temporal)

2.Difference between the subsequent activity (temporal) like  [X2-X1,X3-X2]

3.Difference between the subsequent distance travelled during the activity period (spatial)

4.Pysolo midline crossing data. Data sampling at 1 min interval. number of time fly crosses the virtual midline over the period of 60 s.

Bar: 1.c105;c232-wtb


3. Wtb-TNT


Inter-activity interval of buridan activity


2.Difference between the subsequent activity

Difference between the subsequent distance travelled during the activity period

pysolo midlines crossing



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