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Enhancing Collaboration through Digital Archiving with MIDAS Kitware Inc.

Discover how MIDAS kit redefines digital archiving with its web-based platform enabling storage, search & management of media, fostering collaboration among research teams. Learn about its features, technology, server-side processing, visualization, and ongoing projects. Explore the distributed computing and online monitoring capabilities, along with its deliverables like open-source software, profile editor, and integration with NBIA database for effective data processing.

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Enhancing Collaboration through Digital Archiving with MIDAS Kitware Inc.

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  1. Digital Archiving and Processing with MIDAS Kitware Inc.

  2. Motivation • Scientific datasets are becoming larger and larger (increasing resolution, new modalities, …) • Storing datasets is the first step but querying and retrieving them is even more important • Related documents should be stored along with the corresponding datasets • Data without metadata are useless • Distributed and remote computing is becoming a necessity • Distributed visualization is an emerging technology • Goal is to increase collaboration between research teams

  3. What is MIDAS? • Web-based Multimedia Digital Archiving System • Store, search and manage digital media • Open Source (BSD) • Started in 2005, based on DSpace • Modular and highly customizable Framework • Provides an external API to access media: REST, C++ • Provides server side processing via distributed computing • Provides online visualization • MIDAS features • - Large datasets • - Image Gallery • - Download/Processing carts • - Handle system • - OAI-PMH • - MIDAS-FS

  4. MIDAS Data Server /assetstore/01/10/19/01101909874657394

  5. MIDAS Technology • Server for storing and managing digital content • - Apache (www) • - PostgreSQL/MySQL (database) • Web 2.0 technology • - PHP • - Ajax • - Flash • - Unit testing (integrated with CDash) • Clients • - Web API (REST API) • - Standalone Client (MidasDesktop) • - C++ API • - WebDAV

  6. MIDAS Modules MIDAS Client MIDAS C++ API MIDAS Web API MIDAS Visualization MIDAS Compute Server MIDAS e-journal Publication DB MIDAS Data Server MIDAS Core Apache PostGreSQL File System

  7. Server Side Processing

  8. Server Side Processing • Distributed computing using BatchMake (www.batchmake.org) • Support for Condor Grid • Online selection of datasets and tasks • Online monitoring of grid processing jobs • Online reporting

  9. Ongoing Work • Phase II NIH STTR: Murine Imaging with Martin Styner at UNC • Server-side processing on neural imagery from rodents • NIH NLM A2D2 SCORE • Segmentation validation framework within built on MIDAS • Phase I NIH STTR: COVALIC • Fully featured segmentation validation and method repository built on MIDAS and IJ technologies

  10. Kitware Deliverables • Aim 2.1 : Y1/Q3 – Y2/Q1 • Open-source Software: Demonstrator • Aim 2.2 : Y2/Q1 – Y4/Q3 • Open-source Software: Profile Editor • Open-source Software: MIDAS interfaced with the NBIA database • Open-source Software: Batch processing workflow interfaced with the Algorithm Validation Toolkit • Open-source Software: “Dashboard” in MIDAS • Open-source Software: Integrate the “R” statistical package • Aim 2.2 : Y4/Q3 – Y5/Q4 • Active Dissemination

  11. Project Demonstrator • Import a dataset from NBIA into MIDAS • Done using NBIAAdapter, a Java CLI Application • Set up XML descriptions of seed points and ROIs (AIM) • Run the lesion sizing toolkit algorithm on the dataset using Batchmake • Create a performance report (AVT)

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