Multi-Worm Behaviour Tracker
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luigiferiani and ver228 Blobs ram linux (#53)
* fixed a bug with warning(s)

* compressVideo.py: switched to opencv for median blur

* .gitignore: do not track profile and debugger files

* debug_tests: my folder for testing things and doing debugging. Not useful for Tierpsy in general, but I want it version controlled

* compress_test.py: added test for fluorescence video, it works

* BackgroundSubtractor.py: new method for subtracting the background, using bitwise not and opencv to avoid type casting

* gitignore: added txt in debug_tests folder

* BackgroundSubtractor: fixed new subtraction method to deal with both single images and buffers

* compress_test.py: updated compression test. However, it is not very useful to test a synthetic, single file, as we found out

* BackgroundSubtractor.py: implemented Avelino's changes to the PR

* getBlobsFeats.py: added a .copy() fixing very high RAM consumption on centOs

* getBlobsFeats.py: added a .copy() fixing very high RAM consumption on centOs
Latest commit 40f378c Nov 19, 2018
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_config.yml Update _config.yml Jun 1, 2017
requirements.txt add requirments files and some tests Sep 15, 2018
setup.py correct windows bug Sep 17, 2018

README.md

Tierpsy Tracker

Tierpsy Tracker is a multi-animal tracker developed in the MRC-LMS Behavioural Genomics Group at Imperial College London. The project combines the throughput of multiworm tracking with the resolution of single worm tracking, which means you can extract detailed phenotypic fingerprints from more animals. A large field of view also makes it possible to analyse collective behaviours that depend on animal interactions. The code is open source and extensible and we have ongoing projects using the tracker to analyse fish, Drosophila larvae, and fluorescently labelled worms.

The easiest way to install Tierpsy Tracker is to use the conda-forge as:

conda install tierpsy -c ver228

For more details see the installation instructions section.

Installation Instructions

How to Use

Algorithm Explanation

Output Files