Bone DVC
Summary
Contact Find a list of contact persons here.
Domain Muscoloskeletal
Description BoneDVC is a workflow developed to compute the displacement field between two stacks of microCT images of a bone specimen under compression. The displacement field is then used to calculate the strain field in the specimen.
Documentation
User’s guide
Scientific articles
Requirements
Computational requirements Programming language: C, Python
Dependencies: Java 1.7 for Taverna and mcr to run compiled Matlab code
Memory requirements: The memory requirement scales with the input size. We performed test registration on images of 10, 100, and 1000MB size. The maximum virtual memory required was 2, 11, and 88GB, respectively.
Disk requirements: Large disk space is required for input and output storage. We tested the workflow with images up to 1GB in size. However, there are plans to use images of 70GB in size.
Complementary tools: Taverna for workflow management, Matlab runtime environment.
Type of software licence Limited
Input requirements Format: TmicroCT images are in .dicm format. Registration parameters are saved in a .txt file
Coming from:
Disk use: Two images and one configuration file for each run.
Output requirements Format: Registered images are saved in .dcim binary format. Strain field is in ASCII format.
Used by:Result files are used for post-processing purposes
Disk use: Each configuration return a registered image of size similar to the input size.
Performance and HPC profile
Parallelism Type of parallelism: Serial
Mode of operation The workflow can be run on the same input images with several different configuration parameters. However, these multiple configurations are processed serially.
Deployed on The workflow has already been deployed on ShARC (USFD tier-3) and ARCHER (EPCC tier-1)
Getting started
Benchmarks and examples
Instructions for running on dedicated platforms