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You are here: Home Community Minutes Meetings March 2009 OMERO Team Meeting

March 2009 OMERO Team Meeting

Attending: Jason, Chris, Brian, Colin, Donald, Ola, Andrew, Jean-Marie, Carlos, Josh. Monday 30th March, Wellcome Trust Building, University of Dundee, UK


With the release of Beta4.0, we want to define our work for the rest of 2009. On the one hand, we have a long list of infrastructure functionality we want to add. On the other, our meetings with Lab and College users over the last few weeks have made it clear that they need complete solutions, and that in many cases, delivering small functionality additions will deliver great benefit to our users.

This meeting will therefore define our activities for the next 6 weeks, in the lead-up to Paris meeting, and decide what infrastructure we will fix, and what functionality we will add in the coming weeks. Note that we can't do everything, or even most of what we will want to do, so compromises will have to be made. Obviously, there will be some synergies here-- making simple ROI measurements and ROI support on server is an example.

To deliver these goals, we need to agree on a work plan. This will likely mean a very integrated work pattern, using the mini-group/iteration system. There will likely be no capacity for side projects, and any diversions will need to be agreed on by all. Most importantly, the natural tendency to focus on your own work, and hold functionality and commit later will have to be put aside.

The following are suggested items of infrastructure and functionality that we can discuss. I am fully aware that all of these are updates to both functionality and infrastructure; the classification is from a user's point of view.

Work Items

ItemFunctionality or Infrastructure Known Use CasesComments
Save ROIs on server Infrastructure Multiple Store in a way that we can then have the ability to query
Build ROI drawing tools Functionality Multiple Drawing tool used to manipulate ROI for measurements, lens, publication etc.
Simple ROI Measurements Functionality StarkLab Gelbands Basic statistics; output to report (excel)
Generate Image with ROI Functionality Multiple Crop images to generate new images (similar to projection) and crop images for publication (similar to photoshop). Combine Cropping and projection.
HCS Viewer Functionality/DB/Model Multiple Adjustment to data model and Database to offer a useful Plate viewer
Server-side histograms Infrastructure Criteria to get out of beta!
ImageJ Linker Infrastructure Multiple Provide simple ImageJ plug-in that allows access to PDI data model, for download of images to ImageJ, and upload of images from ImageJ; include basic metadata (acquisition only)
Make Movie Functionality Multiple Converting a Z-range or T-range to an MPG, using current rendering settings; save MPG as attachment on server
z,x,y Image Slice Functionality Multiple Being able to view a plane through Z/X,Z/Y as well as X/Y.
Split view Functionality Multiple Move client-side logic to server to speed up the process when channels are not RED, GREEN or BLUE.
32-bit rendering Functionality Multiple To be able to view sum projections OMERO needs to be able to render 32-bit images.
Move from BufferedImage to OpenGL in insight Functionality Multiple To fix some of the heapspace problems, performance issues and display limitations(number of images/thumbnails) we need move Insight from using BufferedImage and Java2D to OpenGL. The first step would be to replace the use of BufferedImage in the viewer and potentially time allowing the Thumbnail browser to fix some of these issues.
FLIM Analysis Functionality Swedlow & Lamond Lab (Dundee); French Lab (Imperial) Import FLIM data (define which types), and perform FLIM fits on defined ROIs; output to report
Merge Omero.web and Weblitz Infrastructure Multiple Both started from a common code base but were then developed independently. There is much overlap here.
Share development Functionality Multiple Development of sharing concept on the server (IShare) and client side (1-click share and multi-select checkboxes)
Notification system Infrastructure Multiple Email sender queuing system with persistent messages. Existing notification plugin is set on the client side and does not manage messages properly.
Search uses cases Infrastructure That's the question We are still missing a corpus of search questions which should be supported. Without these, there's no way to teach the indexer how to parse incoming metadata
Server-side spreadsheet service Infrastructure Allow collations and iterations with tabulated results
Integration with mManager Infrastructure Allow users to monitor/control microscope instruments, also the possibility of tying analysis to the microscope to re-focus etc. (See Cari Culver's problem from OMERO.week (Thurs. 19/03)
Importer as an Agent Infrastructure Functionality Multiple Write the importer (file chooser) as an agent.
Monitor folder of FS from client Infrastructure Functionality Multiple Allow user to indicate the folder to watch?
Import multi-file formats Functionality Multiple FS needs to be extended to deal with multiple files, the monitor needs some awareness of file formats.
Distributed FS Functionality Multiple An area on a remote machine should be monitored and files automatically imported.
Archiving intergration Functionality Multiple Facilitating moving older data offline
Import new type of data Infrastructure Multiple Extends import to new type of data e.g. ROI, cvs with analysis results and generate overlays.
Client security Inrastructure HTTPS instructions, SSL configuration, cookies & username/password handling (single-sign on?)
Automatic client updates Software To increase distribution, have clients automatically update themselves from the server
Testing machines Hardware Multiple Set up machines for testing on all 3 platforms (originally planned beginning 09)
HCDC connection Functionality Multiple Suport Karol Kozak's HCDC Machine learning Tools
Videos/ Documentation Vital
File formats Infrastructure Multiple HCS file formats possibly

Any Other Business

  • Builds/Packaging/Testing (Infrastructure) - Originally planned for Q4/2008 (pre-ASCB) but got pushed.
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