2021-10-26
Attending: Will, Jean-Marie, Josh, Dom, Xiaopeng Zhu, Khaled, Frances, June, Wilma, Chris, Andreas, Emil, Melissa, Seb, Jian Ma, Jason, Yang Zhang, Petr, David Stirling, Sarah Aufmkolk,
Start: 2:00 pm UK
Project Status
(2-3 minutes each)
- IDR
- Working towards a new “showcase” page
- initial work will be on GeneToPhenotypes and Compounds covid, stories.
- link to be added here
- NGFF/OKRs
- Will: Looking a spec validation using SchemaSalad See PR ngff#69. Bit separate from JSON-LD, but exploring.
- we’ll need to ship the schema in ome-zarr-py etc.
- Josh: lots of spec issues/PRs being discussed. Need to focus - maybe
- Releases
- Security release rollout (Seb): Glencoe had reported customers upgrading and generally happy. On the OSS side, most things external are updated barring the IDR. Moving towards updating the remaining (internal) services.
- Glencoe
- Commented on an issue that was opened 18 months ago. Possibly some weirdness slipped in during the last security release (2019).
- Kevin noticed some oddnesses marshalling dealing with images that aren’t in a dataset. (Old issue though)
- Community
- Planning starting for EBI Machine Learning/Public Data Course. Provisional schedule week of May 16, 2022
- NGFF paper– anyone got an idea for a cover?
- Abstract submission for 4D Nucleome Meeting (deadline Nov 4) - 2nd week of December
- Jian Ma: been asked for nucleosome browser demo. Combine with IDR/OMERO demo?
Main Topic
- 4D nucleome project.
- Integrate -omics data with Imaging data.
- idr0101 - get image & dataset names/IDs and meta–information via IDR API
- query location of probe sequences from 3D genome seq
- Browse to Shape in IDR
- could improve display of probe seq in IDR
- https://codepen.io/nimezhu/pen/qBXEapq
- http://idr.openmicroscopy.org/webclient/img_detail/13457575/?dataset=15165
- Nice to haves:
- Specification for the storage of columns of location information
- Sarah: could look to integrate the SMLM naming structure with this.
- Yang: it would be great if we can come up with a standard format to store probes locations and associated meta-data of the probe (like the DNA sequence of the probe, X,Y,Z location of the probes in the image). Right now we retreive the whole table of a image. That works for image with hundreds of probes.
- Click on ROI in OMERO/IDR and open the nucleome browser
- Highlight on the nucleome browser and probes within that highlighted region will be marked in the images
- Use nucleome bridge to directly sync interaction between OMERO.web and nucleome browser or other third-party websites
- Josh: cf. https://forum.image.sc/t/ome-ngff-spatial-omics-hackathon/57337/25?u=joshmoore
- J-m: start sharing publicly? Yang: working on the last piece of the manuscript (IDR integration with Nucleome Browser) then we will share (code & manuscript for comments)
