Data Input v2 - RodentDataAnalytics/mwm-ml-gen GitHub Wiki

This section will describe in depth how to fill the required fields of the main GUI in order to start your data analysis.

Contents

  1. Paths & Files Format
  2. Experiment Settings
  3. Experiment Properties
  4. Save and Load Settings

Paths & Files Format

  • Trajectory Raw Data: This field requires a valid path in which your exported data from Ethovision are located. Please note that the folder structure should look like the one shown in the picture.

  • Output Folder: This field requires a valid path which the program will use to store all the generated results and pictures. Upon running the program for the first time a cache folder is generated (full path: '.../mwm-ml-master/cache/) which the program uses as the default output folder. Please be aware that new generated results and figures will overwrite the old ones.

  • Format Fields: The rest of the fields require information from the exported files of Ethovision. Each one of these files should contain a cell specifying the animal id and a sequence of cells specifying the location of the animal over Time in X, Y coordinates. These cells needs to be provide in the same way as it is shown in the picture.

Important note: the ID format cells need to be followed (horizontally) by a cell containing a numeric value. The Rec. Time, X and Y cells need to be followed (vertically) by numeric values any empty or non-numeric values (e.g. ' - ' will be excluded.

Experiment Settings

  • Sessions: A session specifies a complete experimental process composed of days and trials. Each session needs to have unique animal ids but same animal ids can exist in multiple session (in this case the repeated ids will be assigned with another unique ids). Moreover, in order to use multiple sessions then all of them must have the same number of days and trials/day, the same experiment properties and the same file format. The number of sessions is indicated by the number of folders which contain the exported files from Ethovision.

  • Days: Specifies the number of days that the sessions have.

  • Trials per Day: Each day may contain different number of trials that is why the trials of each day needs to be specified.

Important note: the program automatically converts the trials per day to trials per session meaning that if the sequence 4,4,4 is provided then the program requires to find each animal id 12 times (4+4+4) per session. Any animal participated on less or more trials will be excluded.

Experiment Properties

  • Trial Timeout: Specifies the time that the animal has in order to find the platform. Must be provided in seconds.

  • Centre [X,Y]: Specifies the location of the centre of the arena. This information can be obtained from the Ethovision 'background' arena picture.

  • Arena Radius: Specifies the radius of the arena. Must be provided in cm.

  • Platform [X,Y]: Specifies the location of the platform inside the arena. This information can be obtained from the Ethovision 'background' arena picture.

  • Platform Radius: Specifies the radius of the platform. Must be provided in cm.

  • FlipX & FlipY In case the platform appears in the wrong position, ticking one of these two checkboxes or both will position the platform to the correct quadrant.

  • View Arena (Button) Vizualizes the arena.

Important note: after defining the Experiment Properties always vizualize the arena to make sure that your settings are correct.

Save and Load Settings

The Paths & Files Format, Experiment Settings and Experiment Properties can be saved and loaded to and from a MAT file.

  • Save Button: opens a dialog box for saving the above properties to a MAT file.

  • Load Button: opens a dialog box for loading the above properties from a MAT file.