Knowledge Base

8 - File and Profile Management How to create, open, save, back up and restore an experiment. How to open trials/runs for acquisition, classification and visualization and how to add and delete trials/runs. How to create, activate, duplicate, rename and delete profiles. You can export (raw) run data, run statistics, trial statistics, group statistics, run visualizations and run videos. 8 - File and Profile Management

8.1 CatWalk Experiments

Create, Open And Save Experiments

Create a new experiment

1. Do one of the following: In the Application Startup Tasks window, select Create a new experiment. Choose File > New Experiment. Click the New Experiment icon in the tool bar.
2. Select an Experiment Setup profile from the Setup Profile list.
3. Enter the Name for your experiment.
4. Accept the default location or browse to a new location. Optionally, you can add a Description and enter a name in the Created by field. The default experiment folder is C:\Users\Public(Public) Documents\Noldus\ CatWalk XT\Experiments.
5. Click Create experiment. The experiment (*.cwe) is stored in a folder with the same name as the experiment.

Open a CatWalk XT 10.7 experiment

1. To open an experiment, do one of the following: In the Acquisition Startup Tasks window, click an existing experiment listed under Open an existing experiment or click Open another... . Choose File > Open Experiment (Ctrl+O) or click the Open Experiment icon.
2. Double-click the experiment folder, select the *.cwe file and click Open.

Open a CatWalk XT 8/9/10.0/10.5/10.6 experiment

When you open an old experiment, it is converted to a CatWalk XT 10.7 experiment. Once the experiment is converted, it cannot be opened anymore in the previous version. It is not possible to open or import experiments from CatWalk 7.x or earlier. Before opening a CatWalk XT 8/9/10.0/10.5/10.6 experiment in CatWalk XT 10.7, you are required to make a backup of the experiment that can still be opened in the previous version. Make sure to store backups in a safe location. 8 - File and Profile Management We strongly recommend that you backup your experiments every day, and, for irreplaceable data, more often. 1. Choose File > Open Experiment. 2. In the window that appears, click Yes. 3. In the Backup Experiment window, you can enter the name and folder for the experiment backup. The file name for the backup contains the current date and time. Click Backup to create a backup copy of the experiment and then click OK. 4. If you convert a CatWalk XT 8 experiment, you can select Rat or Mouse in the Animal Type window. Selection of the type of animal is important for Automatic Footprint Classification and for calculation of the Sciatic, Tibial and Peroneal Functional Index (for rat and mouse different Automatic Footprint Classification algorithms and different FI formulas are used). You can also later select the animal type in the Experiment Settings if you are not sure at this point which animal type you should select. 5. Click OK to start the conversion. When conversion is completed, the Open Experiment Tasks window opens. Select one of the options to continue or close the window.

Errors during conversion

If an error occurs during conversion, you get an error message "An error occurred during the conversion of experiment [experiment name]". Now do the following: 1. Click OK and Cancel and close CatWalk XT. 2. In Windows Explorer, go to the CatWalk Experiments folder and delete the complete [experiment name] folder which contains the experiment you wanted to convert. Do not try to open the *.cwe file from the [experiment name] folder! 3. Open CatWalk and restore the backup file (see page 149) that was created in step 3 above. Possible causes for a conversion error are: The disk to which you try to save the experiment is full. You do not have write permission for the CatWalk Experiment folder. There is an error in the Experiment or Experiment folder. In this case, send the backup file

Save an experiment

Choose File > Save Experiment or press Ctrl+S, or click the Save icon in the tool bar 8 - File and Profile Management When you save an experiment, all trials and runs are saved. Settings (such as, walkway settings, Preferences, Detection Settings, Acquisition Settings and profiles are only saved when you save and exit the experiment. By default, Auto Save is active and the experiment is automatically saved at 5-minute intervals.

Back Up And Restore An Experiment

Create a backup of the current experiment

1. Choose File > Make Backup or click the Make Backup icon in the tool bar.
2. Accept the default File name and Folder or change these. Before clicking Backup, you can click Open Output Folder so Windows Explorer opens the folder in which the backup (*.cwz) file is saved.
3. Click Backup. A message appears when the Backup file was successfully created.

Restore a Catwalk XT backup (*.cwz) file

1. Choose File > Restore Backup or click the Restore Backup icon in the tool bar. When you first start CatWalk XT, you can also select Restore Backup in the Application Startup Tasks window.
2. Locate the backup file (*.cwz) and click Open.
3. Accept the default CatWalk XT Experiment folder or browse to another folder in which you want to restore the experiment.
4. Click OK. If you open a CatWalk XT 8/9/10.0/10.5/10.6 backup (*.cwz) file, the experiment is converted to CatWalk XT 10.7 (see page 147). 8 - File and Profile Management

8.2 Trials & Runs

Open a trial or run

To open a trial/run, in the Experiment Explorer, right-click a trial or run and select Acquire, Classify, Visualize or View Run Statistics. If you get a message "An error occurred while loading the data of run 'Run#', it means the run is corrupt. We advise you to delete this run (see below).

Delete a trial or run

You cannot delete an active trial/run (shown in bold and blue in the Experiment Explorer). If you want to delete trials/runs, you must do this in CatWalk. If you delete trials/runs in the experiments folder in Windows Explorer, this makes your experiment corrupt. To delete a trial, do one of the following: In the Experiment Explorer, right-click a trial and select Delete. Open the Trial List, select one or more trials and click the Delete Trial(s) button at the bottom. To delete a run, do one of the following: In the Experiment Explorer, right-click a run and select Delete. Open the Acquisition screen, select the corresponding trial and select Live video in the View list. Click one or more runs in the Acquired Runs list and click the Delete Run(s) button. For adding trials, see page 41. For adding runs, see page 58.

8.3 Profiles

This section applies to Experiment Setup profiles, Detection Settings profiles, Data Segmentation profiles and Parameter profiles.

Create a profile

1. Do one of the following: In the Experiment Explorer, right-click Experiment Setup Profiles, Detection Settings Profile, Data Segmentation Profiles or Parameter Profiles, and select Add New Profile. 8 - File and Profile Management

Choose Profiles > Experiment Setup Profile, Detection Settings Profile, Data

Segmentation Profile or Parameter Profile > New. 2. Enter the name of the new profile and click OK.

Open a profile

Do one of the following: In the Experiment Explorer, right-click a profile and select Open.

Choose Profiles > Experiment Setup Profiles, Detection Settings Profile, Data

Segmentation Profiles or Parameter Profile > Open, select a profile from the list and click OK.

Rename a profile

You cannot rename the All Data Segmentation profile and the default All Parameters Parameter profile. 1. In the Experiment Explorer, right-click a profile and select Rename. 2. Type the new name and press Enter.

Duplicate a profile

1. In the Experiment Explorer, right-click a profile and select Duplicate.
2. Type the new name and click OK.

Activate a profile

To activate a profile, in the Experiment Explorer, right-click a profile and select Set as Active.

Delete a profile

You cannot delete an active profile. You can also not delete the default profile. To delete a profile, do one of the following: In the Experiment Explorer, right-click a profile and select Delete.

Choose Profiles > Experiment Setup Profile, Detection Settings Profile, Data

Segmentation Profile or Parameter Profile > Delete, select a profile from the list and click OK. When you delete all Detection Settings profiles, a new default Detection Settings profile is created automatically with default settings (see page 49 for the default values). 8 - File and Profile Management

8.4 Export Data And Results

Export The Run Data

Aim

To export the raw print information for each video frame of a run. Each row corresponds to one video frame (100 per second). 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 data. Delete the runs (Delete a trial or run on page 150) listed in the error message and then export run data.

Procedure

1. In the Visualization or Run Statistics screen, under Trial & Run Selection, select a trial and a run.
2. Choose File >Export > Run Data.
3. In the Export Run Data window (see Figure 8.1), you can export run data for: Active run (Run#) - This exports raw data from one run to an Excel file. All runs from active trial (Trial#) - This exports raw data from all runs in Trial# to an Excel file; each run is saved in a separate sheet. Under Output, choose the File name and export Folder.
4. First, click Open Output Folder and then Export.

The Run Data export file

The Run Data export file is an Excel file containing the following columns: Figure 8.1 The Export Run Data window. In this example only raw data of the active Run1 from Trial1 is exported. 8 - File and Profile Management 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 be 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 (see Delete a trial or run on page 150) and then export Run Statistics. 8 - File and Profile Management

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.

Figure 8.2 The Export Run Statistics

window. In this example, only Trial6 which contains 1 runs is exported. Only the Mean of the parameters from the categories Paw Statistics and Base of Support are exported. 8 - File and Profile Management 4. Under Parameters, select the parameter categories you require. For a description of the categories and their statistics, see page 104). 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. GroupType. GroupDescription. Animal - The animal ID. TimePoint - The time point of acquisition of the run. TimePointDescription. Trial - The trial ID. TrialDescription. Run - The Run ID. RunDescription. RunDuration - The duration of the recorded run. RunAverageSpeed - The average speed of the animal in the recorded run. RunMaximumVariation - The maximum variation in walking speed of the animal in the recorded run. CameraGain - The Camera Gain value that was used during acquisition. GreenIntensityThreshold - 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. WalkwayLength - The length of the defined walkway. Walkway_Width - The width of the defined walkway. 8 - File and Profile Management 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 (Delete a trial or run on page 150) 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.

Figure 8.3 The Export Trial Statistics

window. In this example, only trials with completely classified runs are exported (one trial with 2 runs). 8 - File and Profile Management 3. In the Export Trial Statistics window (see Figure 8.3), under Select data, choose: Export active trial (Trial#) - This exports the combined parameters of runs within this trial. Export all trial - This exports the combined parameters of all 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, the parameter categories you require. For a description of the categories and their statistics, see page 104). 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's 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 - 4.114787182 You find those values in the export file of run statistics. The average 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. Suppose that the values of Phase Dispersions per step in the original runs are as follows: 8 - File and Profile Management As you can see, 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. As a result, the trial average for Phase Dispersion is -6.0385, not 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. GroupType. GroupDescription. Animal - The animal ID. TimePoint - The time point of acquisition of the run. TimePointDescription. Trial - The trial ID. TrialDescription. NumberOfRunsUsedForCalculatingTrialStatistics - The number of exported runs based on the selection chosen in the Export Trial Statistics window (see Figure 8.3). RunDurationMean - The mean run duration of all recorded runs in this trial. RunAverageSpeed_Mean - The average speed of the animal in this trial.

Step

Run 1

Run 2

Run 3

Run 4

Run 5

• 4.0000
• 4.000
• 11.1111
• 8.0000
• 1.3698
• 12.5000
• 8.3333
• 11.5385
• 8.3333
• 7.5000
• 7.6923 3.4483
• 3.0303
• 2.8571
• 21.8750
• 14.2857 0.0000 14.2857 Grand average
• 6.0385 8 - File and Profile Management RunMaximumVariationMean - The average maximum variation in walking speed of the animal in this trial. CameraGain - The Camera Gain value that was used during acquisition.

GreenIntensityThreshold - 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.WalkwayLength - The length of the defined walkway. WalkwayWidth - 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*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 first the runs (Delete a trial or run on page 150) listed in the error message. note A parameter that was not measured is indicated with an empty cell.

Export group statistics for one parameter category (sheet)

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

8 - File and Profile Management 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 first option, the chart is saved as PNG image. If you choose the second option, 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. 8 - File and Profile Management

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 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. 8 - File and Profile Management

Procedure

1. In the Classification or Run Visualizations screen, under Trial & Run Selection, select a trial and a run.
2. Choose File > Export and Run Video.
3. In the Export Run Video window, select to export: Labels - When selected, the labels for all prints are exported. Rectangles - When selected, the rectangles around prints are exported.

Time and frame information - When selected, the overlay text showing the run

number, time and frames is exported. 4. Under Output, select a playback Speed, File name and export Folder. 5. First, click Open Output Folder and then Export. The run video is exported in uncompressed AVI format and plays back at the selected speed. You do not need a codec to play the run video.

---

Source: CatWalk XT 10.7 - Reference Manual