CASABee

CASABee is an open-source tool devoted to the analysis of the sperm motility and concentration in honey bee drones.

Features

• Automatic detection and tracking of motile and static sperms from videos
• Computation of the concentration
• Edit mode to manually label motile and static sperms
• Generation of videos where motile and static sperms are tracked
• Result can be exported to a CSV file

Installation and Execution from sources

Python (version 3.8 or higher) and pip must be installed previously.

The following commands clone the repository, install the requirements and execute the program.

git clone https://github.com/jodivaso/CASABee.git
cd CASABee
pip install -r requirements.txt
python3 CASABee.py

Binary Files

Alternatively, you can obtain the binary files for Windows 10 (64bits) here.

Just download it, unzip and execute CASABee.exe.

Sample videos

Click here to download some sample videos to test the application

Specifications

CASABee has been tested with videos in AVI format. The program has been tested on Windows 10 (64-bit) and Linux (Ubuntu 20.04). There are no specific requirements to use this software, but at least 8GB of RAM are recommended for analyzing large sets of videos. The program makes considerable use of parallelization techniques to speed-up the computations, so a processor with several cores is also recommended.

GUI

The graphical user interface is quite simple. The top bar has four buttons: open videos, reset, export results to CSV and edit mode.

Once a video (or a set of videos) is selected, the analysis starts. Once it finishes, you can click on the video to play it with the labels. Static sperms are labelled in red. Motile sperms are coloured, numbered and tracked in the video.

Edit Mode

The last button of the top bar is the edit mode. Once a video is selected, in that mode one manually label and modify the detected motile and static sperms:

• Pressing the key h one can hide the labels and see the first frame of the video. Releasing the key makes the labels appear again
• New motile sperms can be added by clicking on a point (the center) and dragging to select the radio
• Motile sperms can be deleted: right-click on the center
• Motile sperms can be moved: left-click on the center to select the sperm to be moved, drag and drop to the new position.
• New static sperms can be added: double click on the initial point, click on the next point, click on the next point and so on until finishing with a double-click
• For each cluster of static sperms, there appears the estimated number in magent. One can modify the number by clicking on it
• Each cluster is coloured in yellow when hovering over it
• The results are automatically updated after each change in the edit mode
• The video with the labels is recomputed once finished the edition
• With CTRL + z one can undo the last change

Parameters

The default parameters works well in most cases, but one can also tune the parameters used for the analysis:

• Min radius
• Max radius
• Param1
• Param2
• Mean cell size
• Scale
• Camera height
• Diluent parts

Icons

• The open-video icon was obtained from Papirus development team
• The bee icon was obtained from Flaticon

Acknowledgements

This work was supported by the Spanish MINECO (grants PID2020-112673RB-100 and PID2020-116641GB-I00), and the DGA-FSE (grant A07_17R)