Knowledge Base

Classify the Runs

To open the Classification screen, do one of the following:

• From a Tasks window, select Classify Runs.
• Choose Acquire > Classify Runs.
• In the Experiment Explorer, right-click a trial or run and select Classify.

Classification Settings

If your license of CatWalk XT includes the Automatic Footprint Classification (AFC) module, you can specify Classification Settings:

1. Choose Setup > Classification Settings.
2. In the Classification Settings window, you can select:
   • Reset all assigned labels when applying the AFC – When selected, all labels that you already have assigned manually are reset when you click the Auto Classify button.
   • Only assign a label when the max Intensity is higher than – When selected, prints below the specified pixel intensity threshold are not labeled during automatic classification.

Adjust the Green Intensity Threshold

The Green Intensity Threshold is set in the Detection Settings before acquisition. The Green Intensity Threshold is the minimum pixel intensity that is detected by CatWalk. All pixels below the minimum intensity are not processed by CatWalk XT.

You can increase or decrease the Green Intensity Threshold of a run before classification of the paws, after you have acquired the runs. This can be useful when the Green Intensity Threshold was set too high or too low in the Detection Settings.

To adjust the Green Intensity Threshold:

1. In the Classification screen, under Video, click the Adjust the Green Intensity Threshold button on the right.
2. To adjust the Green Intensity Threshold, move the slider to the desired value. Depending on whether you increase or decrease the Green Intensity Threshold, prints disappear or appear, respectively.
   • When you adjust the Green Intensity Threshold of a run recorded with a previous version of CatWalk XT, the lowest possible value for the Green Intensity Threshold is the value with which the run was acquired.
   • Clicking left or right of the slider on the slider bar moves the slider in steps of 5.
3. When the Current Green Intensity Threshold has the desired value, click OK. The run is now processed with the new Green Intensity Threshold value. Depending on the length of the run and the set Green Intensity Threshold, this can take a few seconds.

Classify the Paw Prints

You can classify paw prints manually and/or automatically. For automatic classification you need the Automatic Footprint Classification (AFC) module, which is available as an add-on to the base version of CatWalk XT.

If you use CatWalk XT with the AFC module, there are two main scenarios:

1. You only want to classify paw prints – You first run the AFC module (see Automatic Classification below) and next manually label prints that have not been classified (see Manual Classification below).
2. You want to label both paw and non-paw prints (such as the knee, the hip or the nose) – First, classify the non-paw prints manually (see Manual Classification below) and next let the AFC module label the paw prints (see Automatic Classification below). If this second scenario applies to you, in the Classification Settings the option Reset all assigned labels when applying the AFC must NOT be selected.

Automatic Classification

1. Select a trial/run by doing one of the following:
   • Under Trial & Run Selection, select a trial and a run from the corresponding lists.
   • In the Experiment Explorer, right-click a run and select Classify.

   The corresponding video jumps to the first frame with an unlabeled print (indicated by the label UN). Check that you have selected the correct classification settings.

2. Click the Auto Classify button.
3. Review the run and, if necessary, manually classify unlabeled prints and correct errors (see below).

Manual Classification

1. Select a trial/run as described in step 1 of Automatic Classification above.
2. To label a print, using the mouse, select a rectangle or draw a larger box around one or more of the rectangles that surround a print and release the mouse button.
3. From the menu, select the appropriate label. As a result, the rectangle around the print becomes green and the new label appears. Repeat steps 2 and 3 until all prints in the frame have been labeled. As a result, CatWalk XT automatically moves to the next frame containing unlabeled prints that do not overlap with already labeled prints.
4. Repeat steps 2 and 3 until you are finished labeling prints.

You can speed up labeling prints by drawing a box around both unlabeled prints and labeled prints that both belong to the same paw. The unlabeled prints are automatically assigned the same label.

You can label all remaining prints in a frame as Junk by either clicking the UN=Junk button or by pressing the ~ key or - key (minus sign) on your keyboard.

You can zoom in/out the Video window for easier labeling of the paws. Press the Zoom in icon or Ctrl+'+' to zoom in, press the Zoom out icon or Ctrl+'-' to zoom out, and Ctrl+'0' to reset the zoom factor.

Combine Two Stances in One

Occasionally, a paw print in a video frame is not detected. As a result, the stance (that is, contact of a paw with the glass plate during one paw placement) of a specific paw is subdivided into two separate stances. In CatWalk XT, these separated stances can be manually combined.

Tip: If you have a lot of these subdivided stances, it might be that your Green Intensity Threshold was set too high in the Detection Settings. Try to decrease the Green Intensity Threshold before proceeding with combining stances.

To combine two stances, right-click on the first stance and select Combine with Next. As a result, the stances are combined and the new stance is now considered to be a single stance, in the Visualization and also in the Run Statistics.

Correct Errors

To Jump to a Print

You can quickly jump to an incorrectly labeled print by doing one of the following:

• In the error list, select an automatically detected error.
• In the Print View, click the boxed print.
• In the Timing View, click the corresponding bar.

The video automatically jumps to the first frame of the corresponding print.

Relabel a Print

1. Draw a box around a labeled print, release the mouse button and select Reset.
2. Draw a box around the now unlabeled print, release the mouse button and select the appropriate label.

Relabel a Complete Frame

1. Click the Reset Frame button. This not only resets the current frame but also the subsequent frames of the current paw prints.
2. Repeat steps 2 and 3 as described in Manual Classification above until all paw prints have been labeled.

Relabel a Complete Run

1. Click the Reset Run button.
2. Repeat steps 2 and 3 as described in Classify the Runs above (either manually or automatically) until the run has been labeled.

Remove or Add a Print

It might be necessary to remove or add a paw print in the following situations:

• A hind paw is placed very close to the ipsilateral front paw which has not been completely lifted yet; as a result, CatWalk XT draws one rectangle around the front paw print and the hind paw print while in fact there should be two separate rectangles (one for the front paw and one for the hind paw).
• The Green Intensity Threshold in the Detection Settings is set too low and/or the animal touches the glass plate with its abdomen. As a result, the animal's abdomen is added to the print of the hind paws.

To correct a situation where prints are incorrectly combined, do the following:

1. Right-click the rectangle and select Remove Print. Continue to do this for all consecutive frames in which prints are incorrectly included in the same rectangle.
2. Go back to the first frame in which you removed a print, draw a box just around one of the paws and select Add Print. Do this for all paw prints in this frame.
   • If all prints have been labeled in the run, the Classification Finished Tasks window might appear. To prevent this window from appearing every time you add a print, select the option Don't show this dialog again during this run's classification session at the bottom of the window.
   • If the newly added print overlaps with an already labeled print, the same label is automatically assigned to the new print. Otherwise, you need to manually assign a label to the print (see Manual Classification above).
3. Continue until all prints have been added.

Classify the Toes

You can classify toes with the Interactive Footprint Measurements add-on module. Toe classification of the hind paws is done by measuring the Toe Spread, Intermediate Toe Spread and Print Length and can be used to calculate the Sciatic Functional Index (SFI). The SFI is commonly used as a tool for the evaluation of the recovery of the sciatic nerve.

• Note: You first need to label a paw print before you can classify its toes.
• Note: You need the Interactive Footprint Measurements module to be able to classify toes.

The following measurements are used in Interactive Footprint Measurements:

• Toe Spread – The distance between the first and fifth toe of a hind paw.
• Intermediate Toe Spread – The distance between the second and fourth toe of a hind paw.
• Print Length – The distance between the third toe and the heel of a hind paw.

To classify the toes:

1. Choose Acquire > Interactive Footprint Measurements.
2. In the Classification screen, select a classified trial and run from the list, or click the Previous/Next buttons to navigate to the trial and run you require.
3. Under Footprint Type Selection, select the paws of which you want to classify the toes.
4. Select the paw print that you want to classify.
5. In the large Footprint view:
   • To measure the Toe Spread, click as close as possible to the center of the first toe, move the mouse cursor as close as possible to the center of the fifth toe and click, and next select Toe Spread from the menu.
   • To measure the Intermediate Toe Spread, click as close as possible to the center of the second toe, move the mouse cursor as close as possible to the center of the fourth toe and click, and next select Intermediate Toe Spread from the menu.
   • To measure the Print Length, click as close as possible to the center of the second toe, move the cursor as close as possible to the heel of the paw print and click, and next select Print Length from the menu.

   When you have done two measurements, the third measurement is automatically assigned the remaining label. To remove a line, position the mouse cursor on the line so the cursor becomes a hand icon, click and select Remove. Under Parameters, select the Show parameter values option to display the values.

6. Under Functional Index Settings at the bottom, select the experimental paw from the list.

Viewing Results

In the Classification screen, you can view the graphical and numerical results during classification of runs.

Graphical Results

• Print View – This view displays the paw prints and prints of other body parts.
• Timing View – This view displays the time-based gait diagram. The colored bars represent contact with the glass plate of the paws or other body parts. The gait diagram is displayed from left to right, irrespective of the animal's direction of movement.

You can quickly jump to the first frame of a print by clicking the corresponding print in either the Print View or Timing View.

Tip: Right-click the Print View and choose one of the options to view the footprints in different colors. For example, choose Switch to 'Colorized' mode to display the prints in the preferred colors (File > Preferences > Colors).

Numerical Results

The numerical results sheet displays a number of basic CatWalk XT parameters for each paw print. When you click on a row in the sheet, the video jumps to the first frame of the corresponding print. The images of complete paw prints are shown in the numerical results sheet; a larger version of these images is displayed next to the Video window.

Source: CatWalk XT 11.0 Quick Start Guide, Noldus Information Technology