HMS Image Management Core

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1 HMS A NEW SERVICE FOR HMS RESEARCHERS Jay Copeland HMS Harvard Medical School

2 The Promise of Data Reuse and Sharing Genomics 2

3 The Current Norm With Image Sharing 3

4 Challenges: Many File and Metadata Formats 4

5 Challenges: Large numbers of files 5

6 Challenges: Moving Image Datasets IBM 305 RAMRAC, the first production hard disk drive. Weighing over one ton it could store 5 MB of data. Introduced in

7 A New Service: HMS A new service offered by HMS IT 2 Year Pilot Project Funded by TnT (Tools and Technology) Committee and HMS IT building on prior support from HiTS/LSP Part of RITS (Research Services) First offering: 7

8 Import Store and Protect Organize View Analyze Publish Export Collaborate source: openmicroscopy.org 8

9 Open Science Built On Open Source Secure APIs for Java, C++, Python, Matlab, Web Data Integrity Extensible Efficiency Convenience Enables Collaboration and Sharing Effectively Leverages Existing HMS Resources source: openmicroscopy.org 9

10 Web Application Example: HMS LINCS DB One Dataset: 25,920 images (720 conditions, 4 channels, 9 replicates) All images in the dataset are accessible 10

11 Web Application Example: HMS LINCS DB One Dataset: 25,920 images (720 conditions, 4 channels, 9 replicates) All images in the dataset are accessible Experimental conditions are stored with each image using a powerful Bulk Annotations utility 11

12 Using OMERO to Improve Workflows Typical Pattern: Multiplicity of files, often duplicates Analysis creates additional files separate from original data Replicating and documenting the process is difficult Analysis code is not shared Ad- hoc storage: 12

13 High Performance Workflow Architecture Using OMERO Acquire Data Image & Data Analysis Core Design Analysis Run Analysis Users Import Data To OMERO (In-Place) OMERO Distributed Parallel Filesystem Orchestra Cluster Read Image Data OMERO Database Read Metadata Attach Results source: Douglas Russell 13

14 Proof of Concept: Image Analysis By IDAC of 23K Image Dataset Produced by LSP Using Orchestra Cluster and OMERO Plate- level analysis results attached as files 20 x 384 well plates x 3 replicate fields = 23,040 images 14

15 Proof of Concept: Image Analysis By IDAC of 23K Image Dataset Produced by LSP Using Orchestra Cluster and OMERO Original Image Showing Nuclear Stain Original images and analysis results stored together for quality control, review, sharing, collaboration, and publishing. 15

16 Proof of Concept: Image Analysis By IDAC of 23K Image Dataset Produced by LSP Using Orchestra Cluster and OMERO Original Image Showing Nuclear Stain With Binary Mask Overlay Showing Segmentation Original images and analysis results stored together for quality control, review, sharing, collaboration, and publishing. 16

17 Acknowledgements Chris Botka, HMS IT Caroline Shamu, ICCB- L Peter Sorger, HiTS/LSP Mason Miranda, RITS Douglas Russell, HMS IT/LSP Glencoe Software Tiao Xie, IDAC Mario Niepel, LSP Funding: HMS TnT Committee NIH Grant U54 HL for initial development of LINCS- OMERO HMS IT HiTS/LSP 17

18 For additional information: HMS : (Available December 2015) Open Microscopy Environment: Questions and inquiries: jay_copeland@hms.harvard.edu 18