Walkthrough

This walkthrough demonstrates alignment process with corgie. In this walkthrough, you will align a demo stack stored in a publicly accessible GCS bucket. The example stack consists of one mask layer and one image layer. The data range of the stack is X: 150000-200000, Y: 150000-200000, Z: 170000-17050.

You can visualize the demo stack using this Neuroglancer link.

This walkthrough is divided into two stages: stack preparation and alignment. During the stack preparation stage, you will make a copy of a cutout from the stack, downsample the cutout to a coarser resolution, and normalize the image data. After the stack preparation stage, you will run align the cutout with two different alignment approaches.

Contents

• Set Up Walkthrough Data Path
  • Using Local Directory
  • Using Cloud Storage
• Copy
• Downsample
• Normalize
• Align
  • Block Matching
  • SEAMLeSS
• Render High Resolution Images
• Next Steps