Release Notes

ShapeWorks 5.5.0 - 2020-10-15

What's New

User's Support

  • Revamped documentation: New documentation to support both end-users and open-source developer community in one easily navigable place. This documentation includes background information about statistical shape modeling, the scientific premise of ShapeWorks, and how to get started. It also demonstrates the latest software features, exemplar use cases, and instructions to build/install ShapeWorks.

  • Optimized shape models for use cases: All datasets on the ShapeWorks Data Portal now have the shape model output from running the use cases with a corresponding analyze.xml for launching Studio. Users can cd to where the data is extracted and call ShapeWorksStudio analyze.xml to visualize these shape models.

ShapeWorks Back-end

  • ShapeWorks directly on meshes: ShapeWorks now supports particle optimization directly on triangular surface meshes. This mesh support also enables working with open meshes without additional user inputs. See ShapeWorks Directly on Meshes for more details. For exemplar use cases, see Femur Mesh: SSM directly from meshes and Lumps: SSM directly from meshes to learn how to get started. This mesh support allows for significant memory savings (9.2GB to 53MB in the femur use case).

  • New ShapeWorks API: Consolidation of image-based and segmentation-based grooming tools that creates a stable and reusable API making it much easier and more flexible for users to groom their datasets. This includes a full complement of unit tests. See ShapeWorks API for more details.

All-in-one Studio Front-end

  • Feature maps support: Studio supports the integration of 3d volume feature maps to map imaging data to the optimized shape model. See New in ShapeWorksStudio for more details.

  • New interface for group analysis: Studio supports group definitions from spreadsheets. The new interface supports multiple group sets within the same project file and categorical groups compared to the old binary groups (i.e., yes/no) setting. See New in ShapeWorksStudio for more details.

  • User notes in Studio: Studio stores/loads a rich text notes section in the spreadsheet.

Deep Learning & Shape Modeling

  • New Python package for model-based data augmentation: A Python package for data augmentation has been added. See Data Augmentation for Deep Learning for more details.

  • DeepSSM Python package: A Python package has been added for a deep learning framework that estimates statistical representations of shape directly from unsegmented images once trained. See SSMs Directly from Images for more details.

  • New DeepSSM use case: We added a new use case called deep_ssm that demonstrates data augmentation and deep learning on the femur data. See Femur SSM Directly from Images for more details.

Improvements

User's Support

  • Improved data/output organization for use cases: Use case organization has been updated such that downloaded data goes into one folder (ShapeWorks/Examples/Python/Data/) and use case output goes into another (ShapeWorks/Examples/Python/Output/). This organization will avoid re-downloading use case datasets if the user deleted the output folder.

  • Enable only-shape data for the femur use case: Femur use case demonstrates the processing workflow starting from surface meshes and can now be run without grooming images (in case they are not available). To groom with images, use the --start_with_image_and_segmentation_data tag. If this tag is not included, images will not be used in grooming.

ShapeWorks Back-end

  • Improved constrained particle optimization: An improved implementation for cutting planes that support single and multiple cutting planes per sample has been added. This can be used in modeling scenarios where statistical modeling/analysis is needed for a region-of-interest on the anatomy/object-class at hand without having to affect the input data. See Ellipsoid: Cutting Planes and Femur with Cutting Planes for exemplar use cases.

All-in-one Studio Front-end

  • Improved interface design for Studio: User interface improvements to Studio have been added. These improvements include collapsable analysis panels to improve screen usability, a cleaner file menu, an about box that shows website information and software version, and a splash screen that enables the opening of new/recent projects.

Fixes

ShapeWorks Back-end

  • Constraint-aware particles initialization and optimization: The initialization and optimization steps now respect the user-defined constraints when using signed distance transforms. Hence, at no point, particles will violate the constraints, allowing for arbitrarily defined cutting planes.

  • Constraint-aware particles splitting: Added constraint aware particle splitting for signed distance transforms. The particle splitting only occurred towards a single quadrant. This is fixed by allowing particle splits to shift in a different direction for each particle in every domain.

  • Constraint-aware particle projection: Projecting particles on the surface while manipulating/optimizing particle position now respects the user-defined constraints.

ShapeWorks 5.4.1 - 2020-06-15

Fixes

  • ShapeWorksStudio: Fixed crash when importing data on a new/blank project.

ShapeWorks 5.4.0 - 2020-06-10

What's New

  • New, flexible ShapeWorks project file format: New spreadsheet (XLSX) based project file format that can easily handle multiple shape modeling scenarios. It is now fully integrated into Studio. See the ellipsoid studio example in Examples/Studio/ellipsoid.xlsx for an example.
  • Exporting shape parameters: Added PCA Raw Component Score Export to Studio.
  • New Getting Started documentation: New Getting started documentation goes over shape modeling workflow documentation, different ShapeWorks interfaces with a video illustration for Studio.
  • Lower memory footprint and faster optimization: ShapeWorks is now using OpenVDB, a more memory-efficient data structure, for signed distance transforms. Along with other refactoring and code optimizations, ShapeWorks now uses 85% less memory (from 57.09GB to 9.67GB in one use case). Additionally, the particle optimizer is now 2X faster.
  • Automated development builds: We now offer up-to-date development binary builds that track the master branch, available here. Please understand that these are in-progress development builds, not official releases.

Improvements

  • Improved scalability for Studio: Files now loaded on-demand as necessary.
  • Restructured datasets portal: Better and more consistent directory structure for use cases datasets. See datasets guidelines for more details. Visit our ShapeWorks Portal to register and download datasets to run use cases.
  • Lower memory footprint for estimating correspondences for new shapes on existing shape models: For usage, only distance transforms for the new shapes will be loaded.
  • Improved use case documentation: Better documentation for the RunUseCase input arguments.
  • Documentation for running existing shape models: Added instructions on how to load a pre-trained shape model without running the full pipeline.
  • Consistent cross-platform splitting direction: Correspondence point splits take a random direction, but are now consistent and repeatable across platforms for reproducible shape models.

Fixes

  • Mesh export in Studio: Changed exported meshes to be compatible with CloudCompare

ShapeWorks 5.3.0 - 2020-02-20

What's New

  • Use cases: Added fixed domains use case that demonstrates adding a single shape to an existing shape model
  • Use cases: Added ellipsoid evaluation use that demonstrates the quantitative evaluation of the ellipsoid
  • New commands: Added commands to the shapeworks executable to quantitatively evaluate shape models: read-particle-system, compactness, generalization, specificity
  • New shapeworks executables commands: read-image, write-image, antialias, isoresample, binarize, recenter-image, pad.
  • New build method: Separate build_dependencies script (see Documentation/Build/BUILD.md)

Improvements

  • Use cases: Updated femur use case with an interactive cutting plane selection
  • Studio: Replaced bar chart with explained variance chart

ShapeWorks 5.2.2 - 2020-01-09

Fixes

  • Returned to superbuild.sh build process
  • Fixed non-Qt build
  • Fixed Windows conda_installs.bat
  • Studio: Fixed import and processing of non-RAI image volumes
  • Studio: Fix centering of groomed and reconstructed volumes

ShapeWorks 5.2.1 - 2019-11-09

Fixes

  • Fix examples, binaries

ShapeWorks 5.2.0 - 2019-11-07

What's New

  • Studio: Added live particle optimization updates
  • Studio: Added "Stop optimization" button
  • Use cases: Added a femur use case that demonstrates grooming surface meshes along with imaging data for shape modeling
  • Use cases: Added a left atrium use case that demonstrates grooming images data along with shape data and build multi-scale shape models
  • Use cases: New portal downloadable example data (ellipsoid, left atrium, and femurs)
  • Windows installer and binary releases for Mac and Linux
  • CMake-based superbuild with all dependencies built automatically

Improvements

  • Studio: Added support for reading View2 parameter files
  • Studio: Added legacy (View2) surface reconstructor
  • Studio: Replaced optimization library with same used by ShapeWorksRun

Fixes

  • Studio: Fixes crashes on exit during optimizations (clean shutdown of threads)