Laurie Goodman: Sharing and Reusing Cell Image Data, ASCB/EMBO 2017 Subgroup S meeting
•Download as PPTX, PDF•
1 like•299 views
Laurie Goodman's pre-prepared slides for the Subgroup S Sharing and Reusing Cell Image Data session at the 2017 ASCB│EMBO meeting in Philadelphia. December 2017
Recommended
More Related Content
What's hot
What's hot (20)
Similar to Laurie Goodman: Sharing and Reusing Cell Image Data, ASCB/EMBO 2017 Subgroup S meeting
Similar to Laurie Goodman: Sharing and Reusing Cell Image Data, ASCB/EMBO 2017 Subgroup S meeting (20)
More from GigaScience, BGI Hong Kong
More from GigaScience, BGI Hong Kong (20)
Recently uploaded
Recently uploaded (20)
Laurie Goodman: Sharing and Reusing Cell Image Data, ASCB/EMBO 2017 Subgroup S meeting
- 1. Publishing Imaging Data Laurie Goodman, PhD Editor-in-Chief, GigaScience Laurie@gigasciencejournal.com ORCID ID: 0000-0001-9724-5976 Twitter: @GigaScience; Personal: @grimhawk1 Availability and Credit 2017 ASCB│EMB0
- 2. GigaScience publishes papers with numerous types of imaging data Cell Biology: Electron microscope, confocal cell signaling, cell painting assay, wound healing time-lapse Neuromaging: fMRI, zebrafish brain stacks MRI: myocardial MRI, cardiac atlas, sea urchins microCT: centipedes, brittle stars, earthworms, flatworms, chameleons… Phenomics: fly wings, leaf shapes Ecology: 400,000 camera trap images Mass Spec Imaging: proteomics & metabolomics
- 3. GigaScience imaging data, continued • Super-resolution, tissue atlas, more microCT • Currently converting CT/MRI/confocal data into STL files and include with the GigaDB entry • 3D visualizer included for suitable data types • Downloadable 3D printer files included in several datasets • Video files also hosted in GigaDB & our youtube channel • In total 26 datasets in GigaDB labeled as “imaging” and 2128 files listed as file type = “image” (about 10% of datasets)
- 4. Rewarding and aiding reproducibility of imaging OMERO: providing access to imaging data…
- 5. The alternative... ...look but don't touch
- 6. Virtual Machines of images + algorithms
- 7. Finding food for machine learning algorithms SCIENTIFIC DATA | 2:150026 | DOI: 10.1038/sdata.2015.26 Lack of suitable, large database means complete dataset from paper cannot be made available to community
- 8. Food for machine learning algorithms >400,000 raw camera trap images in GigaDB A picture is worth a thousand data points: an imagery dataset of paired shrub-open microsites within the Carrizo Plain National Monument Taylor J. Noble et al. GigaScience (2016). https://doi.org/10.1186/s13742-016-0145-2
- 9. Disseminating new types of data
- 10. NO Collaborations with Pensoft & PLOS Cyber-centipedes & virtual worms
- 11. NO
- 12. NO GigaScience, Volume 2, Issue 1, 1 December 2013, Pages 1–3, https://doi.org/10.1186/2047-217X-2-14
- 13. SOURCE USE/REUSE PUBLISH INTEGRATION WITH DOMAIN-SPECIFIC DATABASES VIA ISA-TOOLS NARRATIVE DATA (SOCIAL) MEDIA DATA PRODUCTION Sneddon,T.P., Zhe,X.S., Edmunds,S.C., et al. GigaDB: promoting data dissemination and reproducibility. Database (2014) Vol. 2014: article ID bau018; doi:10.1093/database/bau018
- 14. Thanks to: Scott Edmunds, Executive Editor Nicole Nogoy, Editor Hans Zauner, Assistant Editor Peter Li, Lead Data Manager Chris Hunter, Lead BioCurator Xiao (Jesse) Si Zhe, Database Developer Chris Armit, Data Scientist Mary Ann Tuli, Data Editor @GigaScience facebook.com/GigaScience http://gigasciencejournal.com/blog/ editorial@gigasciencejournal.com database@gigasciencejournal.com Contact us: Follow us: www.gigasciencejournal.com www.gigadb.org Published by: In collaboration with:
Editor's Notes
- OMERO is imaging software commonly used in cell biology, this will be implemented in GigaDV Images – is from the notorious Japanese stem cell study that has been retracted, if they had all the images in OMERO this retraction wouldn’t have happened and peer-reviewers could have identified problems during the review process. JCB already have a DV
- 5
- MRI data looking at blood flow to the myocardium and where the software required to run it are presented as a test bed that can also be downloaded as a virtual hard disk.
- 400,000 camera trap images
- 400,000 camera trap images
- "not just omics", and "can do this for any data type and field, even things like electrophysiology that don't “traditionally share“ and Neuroimaging data (fMRI, CT) Virtual worm is now being used in educational materials – reinvents zoology
- Figure 2. The integrated approach to data dissemination and attribution using the example of the cyber-centipede data rich species description. This paper is first of it’s kind – paper published in the Biodiversity journal, - sequencing data in the SRA (EBI ENA), DNA barcoding data in iBOL, micro-CT imaging in morphbank, and images and videos in morphosource All this data was integrated in one place – GigaDB all with their own DOIs, we also have extra files - such as the raw image stacks (in handy 500 image chunks), unedited videos, ISA-metadata files New generation species description that lets you see the behaviour, gene catalog and even 3D internal workings of a TYPED SPECIMEN from the comfort of your PC, rather than delving 1km underground or the dead version in a jar at a museum