Knowledge Base

File and Profile Management

Run Data Parameters

For each frame, the following parameters are displayed:

• Experiment – Contains the experiment name.
• Group – The name of the treatment group.
• Animal – The animal ID.
• Time Point – The time point of acquisition of the run.
• Trial – The trial ID.
• Run – The run ID.
• Frame – The frame number.
• Time – The time stamp of the frame.

For each paw print the following parameters are displayed for each frame:

• X – The X-coordinate of the center-point of the surrounding print rectangle.
• Y – The Y-coordinate of the center-point of the surrounding print rectangle.
• PrintLength – The length (in X-direction) of the surrounding print rectangle given in the Distance Unit selected in the Preferences.
• PrintWidth – The width (in Y-direction) of the surrounding print rectangle given in the Distance Unit selected in the Preferences.
• PrintArea – The size of the print (including all pixels with an intensity value greater than zero).
• MinIntensity – The minimum intensity found in the print (intensity values of zero excluded).
• MaxIntensity – The maximum intensity found in the print.
• MeanIntensity – The mean intensity found in the print (intensity values of zero excluded).

Export the Run Statistics

Aim

To export the values displayed in the Summary sheet of the Run Statistics screen. Each run is represented by a single row in the export file. You can select the parameters to be exported.

Note: If your experiment contains one or more runs with missing or corrupt data you get an error message when you try to export Run Statistics. Delete the runs listed in the error message and then export Run Statistics.

Export Run Statistics for the Current Run

Choose Analyze > View Run Statistics, select a run, then right-click the sheet you want to export and select Export Sheet to Excel.

Export Statistics for Multiple Runs

1. Choose Analyze > View Run Statistics, then under Trial & Run Selection, select a trial.
2. Choose File > Export > Run Statistics.
3. In the Export Run Statistics window, under Select Data choose:
   • Export All Runs from Active Trial (Trial#) – This exports the statistics from all runs in Trial#. Each run is represented by a row in the Excel export file.
   • Export All Runs from All Trials – This exports the statistics from all runs of all trials in the current experiment. Each run is represented by a row in the Excel export file.
   The number of trials and runs in the current selection are shown under the Select Data options.
4. Under Parameters, select the parameter categories you require. For a description of the categories and their statistics, see the Parameters section.
5. Under Statistics, select to export the Mean and/or the Standard Deviation for each statistic from the parameter categories.
6. Under Output, choose the File name and export Folder.
7. First, click Open Output Folder and then Export.

The Run Statistics Export File

This is an Excel file containing the following columns:

• Experiment – Contains the experiment name.
• Group – The name of the treatment group.
• Group_Type
• Group_Description
• Animal – The animal ID.
• Time_Point – The time point of acquisition of the run.
• Time_Point_Description
• Trial – The trial ID.
• Trial_Description
• Run – The run ID.
• Run_Description
• Run_Duration – The duration of the recorded run.
• Run_Average_Speed – The average speed of the animal in the recorded run.
• Run_Maximum_Variation – The maximum variation in walking speed of the animal in the recorded run.
• Camera_Gain – The Camera Gain value that was used during acquisition.
• Green_Intensity_Threshold – The Green Intensity Threshold value that was used during acquisition.
• X-Unit – The width of a single pixel as determined during calibration.
• Y-Unit – The height of a single pixel as determined during calibration.
• Walkway_Length – The length of the defined walkway.
• Walkway_Width – The width of the defined walkway.

In the subsequent columns, for each paw print the selected statistics are displayed.

Note: A parameter that was not measured is indicated with an empty cell.

Export the Trial Statistics

Aim

To export the combined parameters of runs within a trial. Each trial is represented by a single row in the export file. You can select the parameters to be exported.

Note: If your experiment contains one or more runs with missing or corrupt data you get an error message when you try to export Trial Statistics. Delete the runs listed in the error message and then export Trial Statistics.

Note: A parameter that was not measured is indicated with an empty cell in the export file.

Procedure

1. In the Run Statistics window, under Trial & Run Selection, select a trial.
2. Choose File > Export > Trial Statistics.
3. In the Export Trial Statistics window, under Select Data, choose:
   • Export Active Trial (Trial#) – This exports the combined parameters of runs within this trial.
   • Export All Trials – This exports the combined parameters of all trials. Each trial is represented by a single row in the Excel export file.
   The number of trials and runs in the current selection are shown under the Select Data options.
4. Under Parameters, select the parameter categories you require. For a description of the categories and their statistics, see the Parameters section.
5. Under Statistics, select to export the Mean and/or the Standard Deviation for each statistic from the parameter categories.
6. Under Output, choose the File name and export Folder.
7. First, click Open Output Folder and then Export.

How Trial Statistics Are Calculated

Trial Statistics are calculated based on all individual paw prints in all the runs of a trial (provided that they are selected for analysis). It is like all runs in a trial are combined in one long run, and then statistics are calculated. Therefore, Trial Statistics are not a simple average of the values reported in the Run Statistics export sheet.

Example 1 – Print Length: To calculate the trial statistic Print Length for the Right Front paw, the Print Length values of all selected Right Front paw prints in that trial are summed up and the result divided by the total number of Right Front paw prints in that trial.

Example 2 – Phase Dispersions: A trial consists of five runs. The run statistics for Phase Dispersions RF->LH are -8.064102564, -2.961685824, -9.991397491, -4.797619048, and -4.114787182. These values are found in the export file of run statistics. The arithmetic mean of these values is -5.9859. However, CatWalk XT reports a slightly different value, -6.0385, as the average for that trial. The reason for this is that the five run values do not have equal weight. Runs 1 and 2 are based on three steps, whereas runs 3 to 5 are based on four steps. CatWalk XT calculates the average by taking the Phase Dispersions values for each step included in the selected runs. Therefore, a run of four steps contributes to the average more than a run of three steps, resulting in a trial average for Phase Dispersion of -6.0385 rather than the arithmetic mean of the per-run averages.

The Trial Statistics Export File

This is an Excel file containing the following columns:

• Experiment – Contains the experiment name.
• Group – The name of the treatment group.
• Group_Type
• Group_Description
• Animal – The animal ID.
• Time_Point – The time point of acquisition of the run.
• Time_Point_Description
• Trial – The trial ID.
• Trial_Description
• NumberOfRunsUsedForCalculatingTrialStatistics – The number of exported runs based on the selection chosen in the Export Trial Statistics window.
• Run_Duration_Mean – The mean run duration of all recorded runs in this trial.
• Run_Average_Speed_Mean – The average speed of the animal in this trial.
• Run_Maximum_Variation_Mean – The average maximum variation in walking speed of the animal in this trial.
• Camera_Gain – The Camera Gain value that was used during acquisition.
• Green_Intensity_Threshold – The Green Intensity Threshold value that was used during acquisition.
• X-Unit – The width of a single pixel as determined during calibration.
• Y-Unit – The height of a single pixel as determined during calibration.
• Walkway_Length – The length of the defined walkway.
• Walkway_Width – The width of the defined walkway.

In the subsequent columns, for each paw print the selected statistics are displayed.

Export the Group Statistics and Charts

Aim

To export the statistics of parameters calculated per treatment group and time point combination to Excel, and one or more parameter charts.

Note: If your experiment contains one or more runs with missing or corrupt data you get an error message when you try to open the Group Statistics and Charts. Delete the runs listed in the error message first.

Note: A parameter that was not measured is indicated with an empty cell.

Export Group Statistics for One Parameter Category

Choose Analyze > View Group Statistics and Charts, right-click the sheet you want to export, and select Export Sheet to Excel.

Export All Group Statistics

1. Do one of the following:
   • Choose Analyze > View Group Statistics and Charts, then click the Export button.
   • Choose File > Export > Group Statistics.
2. Choose a file name (default: [experiment name]_Group Statistics) and destination folder.

The Group Statistics Export File

This is an Excel file with one sheet for each group of parameters (Paw Statistics, Phase Dispersions, etc.). Each sheet contains the following columns:

• Time Point – The name of the time point.
• Treatment Group – The name of the treatment group.

In the subsequent columns, the selected statistics are displayed.

Export a Chart

Right-click the chart you want to export and select Save to File or Copy to Clipboard.

• With the Save to File option, the chart is saved as a PNG image.
• If you choose Copy to Clipboard, paste the chart in the destination program.

Export All Charts

1. Choose File > Export and Charts.
2. Choose a file name (default: [experiment name]_Charts.pdf) and destination folder.
3. Click Open Output Folder to access the folder where the file will be saved.
4. Click Export.

The file is saved as PDF and contains all charts in the Graphical Results.

Export the Run Visualizations

Aim

To export the video, 3D/2D Footprint Intensities, or Footfall Patterns of the current run to a video file.

Procedure

1. In the Run Visualizations screen, select a trial and a run.
2. Choose File > Export > Run Visualizations.
3. Select the Visualizations (Video, 3D/2D Footprint Intensities, Footfall Patterns) you want to export.
4. Under Output, select a playback Speed, File name, and export Folder.
5. First, click Open Output Folder and then Export.

The Run Visualizations file is exported in uncompressed AVI format and plays back at the selected speed. You do not need a codec to play the Run Visualizations video.

Export the Run Video

Aim

To export the video of the current run.