Workflows

The workflow (flow) module combines multiple functions from various modules for ease of use to perform a desired task.

For example, a standard reg/seg analysis could look like this:

First perform registration of whole-brain CLARITY data to ARA:

$ miracl flow reg_clar -h

Then perform segmentation and feature extraction of full resolution CLARITY data:

$ miracl flow seg -h

Or structure tensor analysis:

$ miracl flow sta -h

Note that not all functions have tutorials yet…we are working on it!!!

Table of contents:

• ACE **new feature**
  • Main Inputs
  • CLI
  • Main outputs
  • Example of running ACE on single subject (segmenation + registration + voxelization + warping) (link to sample data):
  • Example of running ACE flow on multiple subjects:
  • Example of running only ACE segmentation module on one single subject (link to sample data):
  • Example of running only ACE cluster wise analysis on voxelized and warped segmentation maps (link to sample data):
  • Jupyter notebook
• CLARITY-Allen registration
  • Main outputs
  • GUI
  • Command-line
  • Visualize results
• STA
  • Main Outputs
  • GUI
  • Command-line
  • Jupyter notebook
• CLARITY segmentation
  • Main outputs
  • GUI
  • Command-line