Short Description

Plugin to analyze MultiCAFE (Multiple CApillary Feeding Experiments) used in Drosophila research. The plugin analyzes time-lapse images and measures consumption from glass capillaries and movements of individual flies.

Combines the functions of Drosotrack and Capillarytrack to deal with groups of observations. Improved excel export & flies detection functions using background creation and subtraction. While DrosoTrack and CapillaryTrack access files through a specific buffer, files are accessed here in virtual mode (provided by Icy).

Documentation

To run this plugin, you will need at least Java 8 (java 1.8 SDK).

 

MultiCAFE (Multiple CApillary Feeding Experiments) are used in Drosophila research to measure how flies feed from capillaries. The main function of this plugin is to analyze stacks of time-lapse images of glass capillaries containing a colored liquid. The plugin detects flies consumption and the position along time of the flies within individual cages.

To follow flies consumption, kymographs are created from each capillary (by drawing a polyline ROI over each capillary) and the upper and lower level of the liquid within each capillary is detected. The kymographs are stored in a folder (results) created as a subdirectory of the image stack directory and additional xml files (MC_Capillary.xml, MCExperiment.xml, …) store different parameters and measures, such as ROIs corresponding to the location of the capillaries on the images, upper and lower liquid levels, flies positions, etc.

The kymographs can be generated with different sampling periods (1 pixel / image or 1 pixel / n images) to make the analysis quicker. The time series corresponding to the top level of the capillaries is further analyzed to extract “gulps”, which are sudden drops of the liquid related to the feeding of the flies.

In addition to measuring levels within capillaries, it is also possible to follow the position of each fly (singled into individual cages), to correlate the feeding and their movements. To do so, cages are defined by the user (2 procedures are available to do it) and flies are detected either from the raw images by using a simple threshold or by looking at the difference between each image and a background image.

MultiCAFE includes more functions than CapillaryTrack and DrosoTrack, to detect, measure and edit the results. It allows users to attach experiment descriptors to each stack of images (1 stack = 1 experiment), and to work on groups of experiments so that building kymographs, detecting levels, gulps or flies can be done with one click without supervision. The results are exported in excel files which can be further analyzed using power pivot tools.

Main program modules:

  1. Multicafe – dialog boxes and user interface (Sequence;, Capillaries, Kymographs, Levels, Cages, Excel)
  2. Sequence – Classes dealing with images and different ROIs and measures (Cage, Capillary, Experiment, lists, options).
  3. Tools – Classes executing calculations, filtering, data handling, charting and excel export (using POI Apache 4.01.1) used in Drosotrack, CapillaryTrack, AreaTrack and MultiCafe. Not interfaced to Protocols.

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Changelog

  • Version 1.0.0.7 • Released on: 2020-10-25 16:38:35
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    Description:

    routines added to clip curves in a cage to the shortest one and to restore curves after clipping

  • Version 1.0.0.6 • Released on: 2020-10-20 10:57:36
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    Description:

    update build kymographs / detect levels / gulps / flies