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Streamlining Biomarker Qualification: Batchmake, LSTK, and AVT Integration

This document outlines the methodologies for executing offline processes necessary for biomarker qualification and validation. It introduces Batchmake, a scripting language designed for constructing data processing pipelines, which generates Condor DAG scripts for workflow management. Additionally, the Lesion-Sizing Toolkit (LSTK) is discussed, featuring baseline segmentation algorithms to enhance data analysis. The AVT tools provide algorithm validation and result analysis using GNU R. This semi-automated approach aims to facilitate demonstrator applications, leveraging the capabilities of MIDAS for digital archiving.

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Streamlining Biomarker Qualification: Batchmake, LSTK, and AVT Integration

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Presentation Transcript

  1. Batch Analysis Planning

  2. Motivation • Run offline processes to enable biomarker qualification, validation, etc.

  3. What is Batchmake? • Scripting language for constructing processing pipelines • Output to Condor DAG scripts. • No processing built-in • No statistics/analysis built-in

  4. What is LSTK? • Lesion-Sizing Toolkit • Baseline segmentation algorithms • Test Application will be run using Batchmake on a set of data from Midas (imported from NBIA

  5. What is AVT? • Tools for algorithm validation • Baseline segmentation • Result analysis (using GNU R) • Batch processing? • GUI Only?

  6. Planning/Goals * Demonstrator with LSTK modules run via Batchmake (Semi-Automated) * Apr. 22, 2010 Digital Archiving with MIDAS

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