2007-11-1 Project-wide 3:45 GMT - NOTE: UK IS ON GMT; ONLY 4 HOURS AHEAD OF EDT
Attending: Alexa, Brian, Cat, Chris, Curtis, Donald, Jean-Marie, Josh, Kevin, Lars, Will, Andrew on the road
Agenda
- ASCB
- Furniture
- Servers and laptops
- Artwork
- OME-XML Data Model:
- CA and Flexible Annotations
- http://openmicroscopy.org Updates ?
- Bio-Formats: status update
- OME-TIFF: status update
- OME 2.6.1: Status update
- OMERO Beta-2.2: status update
- server
- importer
- insight
- webadmin
- Review of who is doing what
- Other
- Hudson
- http://warlock.openmicroscopy.org.uk:5555 for folks within dundee.ac.uk
- Dead link to Hudson Gallery on old tiki removed
- Links to trac, polls svn, slices, dices, etc. (findbugs, checkstyle, coverage reports)
- Hudson
Notes
- ascb
- how many servers needed?
- need another computer?
- chat offline on that. (no andrew or jason)
- otherwise, all set.
- andrew
- everything as one reimbursement to kevin
- artwork: david's suggestion not for mixed audience
- have to look fashionable and not cheap
- kevin handling getting posters there
- data model
- curtis: curious what this is referring to.
- chris: trying to get some of will's stuff into CAs
- undeclared rules
- what happens to ome-server, or bioformats if there's another top-level block
- curtis: don't know. can't test.
- or try imagej bioformats importer
- Will: can produce files using the top-level file.
- - http://users.openmicroscopy.org.uk/~will/ should contain files soon.
- trivial test: on sample.ome with garbage, barfs in bioformats
- seems to work in ome-server
- Would a non-ome block first barf?
- What happens with two ome blocks?
- andrew
- what schema's do we provide?
- would like to have a DAG with no backlinks (SPW-->OME-->SPW, same with analysis module)
- documentation is technically correct, but not very clear
- after next release, start to get doc moved over and rewritten
- possibly a schema along for internal references
- two ways to add data
- write valid CA and STD file
- write outside of block
- curtis: like strengthening the CA block contract (docs)
- ome-validator: what's the complexity of that? (curtis)
- largely, mostly technical issues. and getting the error reporting good
- also does some high-level checks. number of planes in tiff/binary data
- bioformats can do some of this.
- similarly to recently written validator?
- http://support.svi.nl/wiki/OmeValidator
- @try to get source code
- openmicroscopy.org
- all files moved out of TestImages
- stripped files from www.openmicroscopy.org (previously for anyone)
- some problems with making everything public
- starting campaign to get one of every file
- perhaps a simple script which defines what's public and gets copied
- feedback: for ome-xml implementors, etc., it's pretty buried
- no screenshots, more examples, pretty deep
- perhaps a video from Loci on XML.
- training site
- similar to what paula is working on
- need to separate user/dev focuses
- dev are users, too.
- data is spread about a bit: loci, ome-xml.org, openmicroscopy.org
- andrew should let curtis know if he wants help with ome-xml
- bio-formats / ome-tiff
- revamping interfaces to handle 2007 stuff
- problem is building old stuff and new stuff in parallel
- haphazard method adding to MetadataStore
- trying to autogenerate that code, too.
- issue of methods which take 20/30 methods
- possibility of using builders
- e.g. someLongMethod(a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p) becomes
- shortMethod(new SimpleBuilder().setABC(a,b,c).setMNOP(m,n,o,p)); // rest null
- do we deprecate interfaces?
- one complaint about stability of bio-formats
- volocity
- ome-tiff support. someone is trying to convert, and emails are comming with errors.
- how do we determine if something is "OME-approved"?
- links on our webpage
- need to be cautious about what we can help to support
- another star ranking system?
- don't say "partial" but "yes, but doesn't support a,b,c"
- what is "OME-XML" or "OME-TIFF" support?
- curtis looking into issue, what's causing it.
- trying to work it out
- multiple tiff files
- scanning images in a directory
- images/pixels ids
- if lsid, no problem. internal, causes an issue.
- can't match across tiff files.
- rule: "must use an lsid if you are spreading among files"
- for some form of file mangaling
- "strongly encouraged"
- 2.6.1
- couple small things that curtis wants to look into
- omero
- waiting on float4 widening (OMERO35-->OMERO37)
- remoting errors. seems to not be happening with the jar. (4.2.1 has 2.2.1)
- background thread seems to make valewalker happy
- formats
- http://trac.openmicroscopy.org.uk/omero/wiki/ImporterFormats is the list going in
- perhaps few small changes
- ome-xml will be in 3beta3
- want to also support split schemas in bioformats and then in importer
- insight has been ready since middle of the weak
- needs to upgrade user guide with formats
- webadmin: no changes everything fine
- pack this week; integration testing next week