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Reproducibility

This section aims to make it possible for any user to reproduce all outputs of this plugin present in this documentation.

All file mentions (with this format) refer to the file structure of the provided test data.

Test Data

DOI

Test data is available in this repository. Notably:

  • Adults
    • Gutter/Track (short and long versions)
    • Plus Maze
    • Tank (sideways recording)
    • Tracking data
  • Larvae
    • Six-well plate (short and long versions)
    • Tracking data

These may be used to experiment on the plugin's capabilities or simply to get used to the workflows.

Distributed under the CC BY 4.0 License

2 - Processing

Binary Heatmap Image

larvae/larvae-long.mp4 file was inputted in this processing tool.

The whole video was set as the interval, rendering the output shown.

Minor cropping and rotation adjustments were done.

Sum Heatmap Images

adults/adults-long.mp4 file was inputted in this processing tool.

Lookup table was set to Fire.

The start interval was chosen (1-5400).

roi.roi was loaded into ROI Manager.

Minor cropping adjustments were done, rendering the output.

Sum Heatmap Video

adults/adults-long.mp4 file was inputted in this processing tool.

Lookup table was set to Fire.

The whole video was set as the interval.

roi.roi was loaded into ROI Manager.

Rendering the output.

3 - Analysis

Calculate Score Gradient

Files adults/tracking/full.xml and adults/tracking/adults-tracking.avi were inputted into this tool.

Fix missing spots and Display Plots were left enabled.

Max and Min values were loaded from the XML file using the dedicated button.

Rendering the plots shown

Calculate Score Sectors

Files adults/tracking/full.xml and adults/tracking/adults-tracking.avi were inputted into this tool.

adults/tracking/sectors.zip was opened in ROI Manager.

Fix missing spots and Display Plots were left enabled.

Rendering the plot shown.

Extract Tracking Frequency Data

Using this plugin's FFmpeg tool, larvae/larvae-short.mp4 was cropped 200 frames from the start and util frame 501, using the Well_2 ROI from the larvae/RoiSet.zip file.

The output was processed with larvae tracking, generating the larvae/tracking/larvae-tracking.avi file as its output.

The video scale was set to millimeters. 1 px equivalent to 0.042270531400966184 mm

The latter file was run through Trackmate. Its output created the larvae/tracking/full.xml file.

Then, larvae/tracking/full.xml and larvae/tracking/larvae-tracking.avi were inputted into this analysis tool.

Display Plots was left enabled.

Generating the plot shown.

Quantify Binary Heatmap

larvae/larvae-long.mp4 file was inputted in the Binary Heatmap Image processing plugin. The whole video was set as the interval.

Its output was inputted into this analysis tool.

larvae/RoiSet.zip was opened in ROI Manager.

Display Plots was left enabled.

Rendering the plots shown.

Thigmotaxis

Files larvae/tracking/full.xml and larvae/tracking/larvae-tracking.avi were inputted into this tool.

Area percentage was set to 50%.

Open Frame button was pressed, then the image was calibrated to millimeters. 1 px equivalent to 0.042270531400966184 mm

A ROI enclosing the whole image was created.

Fix missing spots and Display Plots were left enabled.

Creating the plots shown.