Adjust Image

Track workflow - step 3

Threshold Level

The threshold level is the intensity value WormLab used for separating the background and foreground of the image. Worms appear in the foreground, while other objects (e.g., the agar plate) appear in the background.

To change the level manually, drag the slider or type a value.

WormLab highlights the areas identified as foreground in green to give you an indication of how well the thresholding corresponds to the original image. To turn off the highlight, click the Highlight button.

Auto-detect

Use the Auto-Detect button (bottom of the panel) to automatically optimize thresholding.

To enable auto-detect, define scaling in the Set sequence info step. Only accurate scaling can ensure proper thresholding and valid data.

Image Processing

ClosedBackground smoothing

Use when the background is spotty.

  • Refine the threshold level after applying smoothing.
ClosedFill holes

Use to fills holes within the worm regions while keeping the initial region size.

The size of this operator should always be less than 1/3 (one third) of the width of the worms.

This tool refers to the morphological closing of the binary image (dilation followed by erosion).

ClosedGaussian smoothing

Use to perform a Gaussian blur on the images.

Gaussian blur reduces signal noise in the image, but it also reduces detail. It smooths worm contours and reduces "holes" within the object region.

The value should be less than 1/3-1/4 of the width of the smallest worm.

ClosedHotspot illumination correction

Use when there is a bright spot or uneven illumination in your image.

Recommended for large field of view such as whole plate.

ClosedSmall object filter

Use to remove tiny foreground objects. This tool is most effective when the size of the worms is significantly greater than the size of the objects.

The range for this filter is 1-10 but we suggest that you try low values. Values greater than 2 tend to erode the tail and head of the worms.

This tool refers to the morphological opening of the binary image (erosion followed by dilation).

Integrative Derivative Segmentation

Use for "problem" videos where worms are not well-defined against the background.

ClosedHow to use
  1. Check the I.D. segmentation box.
  2. Adjust the outline factor and the fill factor.
  3. Click Apply to display the adjustments.
  4. If you're satisfied, click Auto-detect.
ClosedOutline factor

Adjust to better distinguish the edges of the worms.

ClosedFill factor

Adjust until the worms appear solid.