2007-02-01 Project-wide 3:30 GMT
Attending: Josh, Chris, Brian, Cat, Curtis, Ilya, Jason, Andrew, Brian
Agenda
- Review of last project-wide meeting? notes/issues
- OMERO Roadmap-- meeting on Feb 7
- OMERO Release Issues-- how often for updates?
- Week-in-review
- Other
From Curtis:
- Status of Bio-Formats with OMERO.importer
- Is current API sufficient? I.e., openBytes method; what about Plane2D?
- OMERO version confusion
- 3.0-M3-Beta1 vs 3.0-Beta1 — downloads page still says Dec '06
- Will try out OMERO next week
- Web site says: "Details on this work [a single integrated data management system that leverages the advantages of both systems] will be available towards the end of Q1/2007" — is someone working out these details?
- Any questions/thoughts about OME Notebook vision or status?
- Possible OME-TIFF spec improvements:
- Change file extension to .ome.tiff [CTR: in favor]
- Store duplicate OME-XML block under custom tag [CTR: in favor]
- Create schema variant for OME-TIFF to eliminate redundancy of certain Pixels attributes (SizeX, SizeY, etc.) — ideally using XML constructs (substitution groups?) that limit duplication between OME-XML and OME-TIFF schema versions [CTR: tentatively against]
- Embed a copy of the OME-XML block encoded within the first image plane; also potentially store an additional "cover page" before the encoded image plane with rendered text offering an explanation and links regarding OME-TIFF. [CTR: strongly against]
- Expand OME-TIFF definition to allow BigTIFF — allows single files larger than 4 GB [CTR: in favor]
Notes
- Last week; nothing (release)
- Feb 7th is planning. Notes will be up then.
- Dicussion in two weeks
- Website
- Issues? (jrs)
- CR: 3.0-M3-Beta1 v. 3.0-Beta1 (fixing other minor website stuff)
- IG: Kudos on the website.
- Issues? (jrs)
- Versioning
- Beta1.1, etc. ? On a weekly basis as things come in.
- BioFormats Integration
- Plane2D and Channel separator
- Need release schedule and tags
- CR: Planned anyway. Can also do self.
- CA: Better if bio-formats team does it.
- IG: Tagging along with API changes?
- CA: Possibly tags/current and get the jars or tags/head for source
- CA: Let's start with tag
- "a single integrated data management system ... (Q1/2007)" ?
- CR: Really?
- JS: Planning on Feb/7
- OME Notebook
- CR: Excited about UsableImage+Notebook
- CM: Try to get to Madison
- OME Tiff changes
- CR: duplicate tags for photoshop
- IG: hash of image rather than duplicate tag
- CA: Editing the file in anyway may invalidates the XML.
- IG: but that's a different image. You have to get it back together.
- CA: tools to compare the XML in the Tiff with the image (timepoint removed, etc.)
- CR: MD5 for each plane?
- CR: Or XML warning "DO NOT EDIT"?
- IG: Not feasible to manage the changes.
- IG/CA/CR: Notebook as the tool to "re-metadate" images.
- CR: Purpose of OME-Tiff is to make it a standalone image (just don't screw it up)
- IG: We only provide the rope.
- CR: BigTiff
- 64bit pointers for +4Gb images
- Minimal differences
- CR: Just allow OME-Tiff to be BigTiff
- OME-XML
- Removing duplication?
- IG: If you are just trying to detect change, use checksums.
- CR: Digets of XML block to detect changes?
- CA: Custom tag with the digest of XML block
- CA: Is this a real concern?
- CR: If there's nothing against the digest, then will be proposed
ActionItems
- Curtis will try to try it out.
- Chris send doc on bio-formats changes to curtis
- Curtis is going to propose OME-Tiff digest and other ideas to list
- Jason and Ilya talk next week.