4. How to perform a nonlinear registration with WebWarp

Last modified by puchades on 2022/12/07 15:46

What is WebWarp?

EBRAINS WebWarp serial section image viewer provides an intuitive way of navigating high-resolution 2D image series coupled with segmentation overlay, from a web browser.  WebWarp allow the users to perform a nonlinear adjustment of the registration obtained with WebAlign.

How to use WebWarp

1. Navigate to the WebWarp app in the left-hand panel: all the .waln files located in the Bucket are displayed on the WebWarp main page.

2. Select the waln file corresponding to your result from the WebAlign image registration or the demo waln file named "demo_mouse_data_waln".

3. Wait for the images to load: this may take some time.

4. Your registered images are visible in the main window.  The atlas regions with transparency sliders can be toggled using the "Atlas opacity" button. The color of the atlas outline can be modified by clicking on the colored rectangle.

5. Place a marker on an area you want to stretch using the space bar. Nonlinear distortions are applied by dragging a marker using the mouse.

6. Press Delete or Backspace to remove a marker under the mouse cursor.

A good strategy is to place markers around the contour of the section first, and then proceed with refining the inner parts.

Try to keep the number of markers to a minimum. Save your markers is allowing you to go back to previous section images.