Getting Started With ShapeWorks Studio

ShapeWorks Studio provides an all-in-one GUI based interface to the ShapeWorks toolkit. In Studio, you can manage input Data, Groom, Optimize and Analyze your data all within a single interface.

Splash Screen

The splash screen provides access to recent projects and an option to create a new blank project.

Data Module

The Data Module shows the project data table, landmarks, constraints as well as user-defined/saved notes. This module enables you to add and remove shapes (segmentations and surface meshes) to your cohort, define anatomical landmarks, place cutting planes and free form constraints for surface exclusion.

See Studio Data Module for more information.

Groom Module

The Groom module provides options to preprocess/groom the input data. Options differ for binary segmentations and meshes. You also have the option of skipping grooming if your data is already prepped.

See Studio Groom Module for more information.

Optimize Module

The Optimize module provides options for the particle-based optimization. After selecting options and clicking "Run Optimize", you can monitor the process of the optimization in real-time. Particle positions will be displayed on individual shapes as they progress where color encodes surface correspondences across different shapes in your cohort.

See Studio Optimize Module for more information.

Analysis Module

After optimization is complete, you may analyze the data in Studio using the Analysis module. There are several panels available in the Analysis Module.

See Studio Analyze Module for more information.

Preferences

Studio provides a number of preference options.

Option	Description
Color Scheme	Base foreground and background colors for viewers
Color Map	Color map used for scalar ranges
Reverse Color Map	Option to reverse the color map
Discrete Color Mode	Option to use discrete colors for color map
Groom Output	Folder name for groom output
Optimize Output	Folder name for optimize particle output
Mesh Cache Enabled	Whether to use a cache of meshes
Mesh Cache Memory to Use	Percentage of phyisical memory to allow mesh cache to use
Mesh Parallel Reconstruction	Whether to use parallelized mesh reconstruction
Mesh Parallel Number of Threads	How many threads to use for parallelized mesh reconstruction
Orientation Marker Type	Medical, Triad, or None
Orientation Marker Corner	Upper Right, Upper Left, Lower Left, Lower Right
PCA Range	Number of standard deviations for PCA slider
Number of PCA Steps	Number of steps for PCA slider bar
Geodesics Cache Size Multiplier	Multiplier value for geodesics caching
Log Location	A display of where the current log file is located
Automatically Check for Updates	Whether Studio should automatically check for updates to ShapeWorks
Send Anonymous Usage Statistics	Whether Studio should send anonymous usage statistics to the ShapeWorks team to help improve the software

Data Collection

ShapeWorks Studio can optionally send anonymous usage statistics to the ShapeWorks team. This data helps the team by providing basic user tracking numbers that we report to funding agencies to help in acquiring additional funding. Additionally, we are prospectively collecting a few usage parameters that may aid in development of particular features. No user data (images, meshes, segmentations, etc) are ever transferred, only basic user event information (e.g. number of times optimize is run).

Viewer Controls

See Studio Viewer Controls for details on viewer controls.

Menus

File Menu

• New Project - Create a new project
• Open Project - Open a project from disk
• Show Project folder - Open Explorer/Finder for project location (windows/mac)
• Save Project - Save project to disk
• Save Project As - Save a copy of the project to a new file
• Import Shapes... - Import new shapes
• Export - See export below
• Up to 8 recent projects are shown at the bottom

Export Menu

See Studio Export Options for details on export options.

Project setup

ShapeWorks Studio and the shapeworks commands groom and optimize store project data in an XLSX spreadsheet. The spreadsheet format profiles a uniform, easy to edit, easy to organize way of inputing data into shapeworks for grooming, optimizing and analyzing data. See Here for more details regaring the project sheet and the python API available to generate the project sheet.