2008-01-25 Omero Review Meeting
Attending: Alexa, Andrew, Carlos, Cat, Colin, Donald, Jason, Jean-Marie, Josh, Melissa, Will
Agenda
- Status Report
- OMERO.server
- OMERO.insight
- Status: interaction with new server
- Directions and evolutions i.e. integrate new Annotation (not only textual working)
- Search
- OMERO.importer
- New file formats?
- OMERO.webadmin
- Protocol Editor
- New name??
- Screenshots and info from NCBO
- Scripting Engine
- Feedback from BioImage Informatics mtg
- Current design and progress
- OMERO-FS
- ome xml
- TiffData - assigning a FilePath attribute
- If you have files image1.tiff, image2.tiff image3.tiff
- In the ome-xml in image1.tiff you can refare to ./image2.tiff and ./image3.tiff
- Is it also ok to refer to itself as image1.tiff rather than not specify a FilePath?
- Location of ImageRef -> move from spw to ome (anyone using this yet)
- TiffData - assigning a FilePath attribute
- Website changes
- Bio-Formats
- Beta 2.3 Notes of Interest
- Downloads--
- The future of scientific data repositories
Notes
- server
- search is coming along well. defining the interface
- need short-term wish list soon
- otherwise can make longer list for b4
- sessions
- coming along; tedious but should be benefitial
- nightshade
- some minor issues but hopefully system related
- otherwise b2.3 trucking along
- upgrades
- all automated bug reports are using older version (b2.1, b2.2)
- @automatic upgrade or @better communication of milestones
- @email registration when they download
- disconnect between ome-users and downloaders
- @dialog to the user that a new version is available
- @have server send email on upgrade
- how
- client connects to dundee
- if new, dialog with need new client (and possibly server)
- then talk to current server and see if compatible.
- jean-marie adds a ticket
- josh moves UpgradeCheck to OMERO
- search is coming along well. defining the interface
- insight
- many changes made
- don't have any images; need new importer
- begin with tagging middle of next week
- first version of UI to get it in front of the user
- are we getting rid of category/group?
- will need to migrate data
- beta3?
- issue with having two DB rows which are the same semantical concept for users
- cat: it would be good to make the jump from a building-the-user-base PoV
- jrs: huge number of categories (legacy data is the big problem)
- cat sets up meetings to get feedback
- UI for search over different types is already in place
- will look into having "saved options" of what types one wants to search for
- searching on pre-defined terms comes later
- structured annotations seems to be resonating
- measurement tool
- probably won't see anything until beta3
- small changes from user perspective
- should be more configurable/customizable
- a partial rewrite; but something that can be used further
- or may need to get tabled for beta3 w.r.t. scripting engine
- what's preventing people from adopting omero is attachment to external tools
- importer
- file formats. 6 of 7 tests for beta 2.4. haven't tested with latest version of code base
- incell. difficulty of SPW
- haven't updated omero metadata store.
- possible to use the previous release?
- bug fixes to all the formats since the big change
- brian back on saturday
- tenatively more testing with 2.4 and out by end of the month
- otherwise, fixing bugs & efficiency
- file formats. 6 of 7 tests for beta 2.4. haven't tested with latest version of code base
- webadmin / web-?
- possibility of resetting enums original values
- need to look into the algorithm, so there's no data loss
- written some preliminary code
- waiting on looking at carlos' code
- needs to get started
- getting new license to carlos to commit the file
- carlos will contact ola when everything committed
- use case: define a set (projects, datasets, ...) in insight (, importer, ...)
- ask server for URL which gets sent to collaborator
- collaborator connects with URL and is shown that set
- josh: use omero sessions for flickr-like links
- possibly something that doesn't exist in our current permissions model
- request coming from tech-agnostic users. just want it.
- need to define what we can do now, and what later
- see blitzconnector.py
- beta 3 is looking around first of may after user testing, etc.
- protocol editor
- no response on email re: new name
- feedback from michael
- integrated with phenote
- need a new movie
- will add links to screenshots
- scripting engine
- bioimage informatics mtg
- good mtg.
- model to support "my data"
- flexibility again
- what can we support?
- what can we make easy?
- structured annotations for analysis was welcomed
- "matlab!"
- ITK/VTK~ bsd license. will discuss later
- donald
- 2 things
- scripting engine
- integrated into the server
- matlab
- allowing people to connect to server from matlab
- scripting engine
- first blast of the projection script
- writing matlab blitz interface & gateway
- to test: need an updated importer
- getting something to these developers, a way in.
- hard parts
- guis
- matlab as server
- 2 things
- bioimage informatics mtg
- colin
- needs to get an idea about interfaces
- what should the omero.fs server expect and pump out
- currently is kicked off my server saying (directory, include, exclude)
- will then send back events saying: ok, X files done done
- colin: will send emails to work things out
- jrs: what does everyone need to make this easier?
- documentation on the python side?
- sufficient to have carlos' work visible?
- colin: need something more
- OME-XML
- completing tickets
- some things need to discuss with people
- "recursive link": image1.tiff refers to itself as ./image1.tiff
- makes logic more generic
- SPW
- moving ImageRef definition between files
- easy to do as long as no one is using it
- jason: don't know, but apparently cellomics says OME-compliant
- have to act assuming someone is using and go through the proper revision process
- "recursive link": image1.tiff refers to itself as ./image1.tiff
- renaming release to february
- @andrew sends a logical view of SPW to josh
- website
- any feedback?
- none. good!
- carlos can help with plone
- jason and andrew reviewing all of web documentation
- migrating tiki->trac: Add "THIS PAGE HAS MOVED" links
- ...and we should start cross-linking our image-informatics efforts
- downloads
- 60 downloads this month
- storing on google
- paris
- tentative: april 29/30th ?
- room better for communicator
- starting to use omero in mid-february with a rollout to super users
- moving day?
- not yet
- mtg. in two weeks
- jason giving talk on 8th.
- let's have a ticket day
- or later on the 22nd?
Action
- upgrade check for clients
- setup user sessions re: tags/category groups