2007-10-18 Project-wide 3:45 BST
Attending: Alexa, Andrew, Brian, Curtis, Donald, Iggie, Jason, Josh, Kevin, Will
Agenda
- ASCB
- OME-XML Data Model: latest changes, updates and versions
- Editing OME-XML Metadata using the protocol editor - what should we allow
- 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
- Deletes - what all should go (statsinfo, lightsettings, etc.)
- bio-formats build
- Should we add a "formats" component on trac?
- Failing tests
- Various.
- RenderingEngineTest - removed
- RenderingSettingsTest - hard coded values
- LdapTest - no ldap. set to manual
- PixBufCreationUnitTest - compile error. fixed.
- PlaneReadUnitTest - "
- PlaneWriteUnitTest - "
Notes
- ASCB
- Getting things together
- booth diagrams, square/round/etc...
- bio-formats
- should try to push OMERO-verification for formats to melissa
- brian: process includes
- gather as many images as possible
- import to omero
- look at viewer
- third party app. to look at it (re: dicom)
- certified files are md5'd and checked from the command-line
- what happened was got some last minute tests
- we should try to get everything into the repository
- brian: process includes
- negative pixels value
- bio-formats should tell us that (int8 v. uint8)
- does omero support the signed types? yes
- display of the dicom images displays incorrectly in loci tools
- @bug
- there will always be corner cases
- usually only hear about it when things go wrong
- would be best to get the extreme cases in while defining the format
- tiff/xml
- Curtis mocked up 2007 Java classes, Chris updated generator
- can start using those in bioformats
- would like to start using "ome.xml.r2007_06.*" package (with subpackages)
- hdf (Eric working on it)
- for spectral
- xml->tree structure
- can split binary into tree in various ways
- eric writes up how things are stored
- TIFF can do tiling
- but multiresolutions? not really.
- cF. seadragon: http://www.ted.com/index.php/talks/view/id/129
- No changes in rendering settings, etc.
- that's our bread and butter
- beautiful, but ...
- but it is a backend for providing scaled data at a high rate
- heads-up for 2.6.1 and formats which aren't working
- bio-formats could be prioritized but is failing some edge cases
- @add tickets please
- htd for example isn't working (one example, with companion file)
- incell difficulties
- certainly stop using perl TIFF importer
- bio-formats: support compression and packed bits
- curtis: brian, you can use the commandline, or even save files with README in data
- @move TestImages from webpage to bio-formats master repository
- all our lsm files are probably the same
- should try to push OMERO-verification for formats to melissa
- b2.2
- just import issues
- videos cover a lot of it
- out by next week, or perhaps monday after
- python
- ilya's getting nibbles
- colin coming soon
- delete
- lightsource hardware
- josh will err on the side of deleting too little
- build
- get rid of svn:externals?
- bioformats-omero would keep them, brian uploads a new jar to skyking
- what should the jar be?
- @brian will commit jars to svn
- add jar to lib/repository
- delete old jars
- update omero.properties version number
- possibly use loci_tools.jar <-- needed for the formats (mdb, etc.)
- might need "ant tools-light"
- for 2.2 brian PINGS josh when it's time to try again
- "formats" component
- use importer instead
- tests
- setup public ldap server??
- try to setup test data
- omero.properties ldap property is false, then don't run test
- anyone test 2.6.1 ldap impl. in Dundee
- ask Chris.
- protocoleditor
- not sure of the scenario of wanting to edit the custom attributes
- experimental protocol/description: free-form<-->miaca
- custom attributes, or something else?
- ilya: having directory structure with files which get all sweeped together
- data types aren't in core model, but there is information
- keeps tracks of genes (external databases, manipulations, probes)
- ... display tool, relies on custom attributes to work
- movie or howto? movie lets us see what the person who built it is working
- validator should ignore the custom attributes
- checked against semantic type definitions?
- STDs could come from different document
- andrew thought you could specify a schema for a separate block. will check.
- ilya: shouldn't be anything you want, just can't define the schema properly
- can use the stylesheets to see the core types as CAs.