2009-04-03 Project-wide Conf call
Agenda
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Beta4.0
- Cleaning up all tickets & closing milestone
- On schedule for 4.0.1? (Windows/DV)
- Moving tickets to 4.0.2?
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Beta4.1
- OMERO SPW extensions and Bio-Formats integration
- Progress made on the user stories?
- Moving tickets & description to 4.2?
- Everything committed on both branches?
- Breaking up the 8+pt stories?
- Nitpick e-mail from Curtis "ROIs in the XML schema"
Attending
- Carlos, Colin, Curtis, Dundee (Jason, Chris, Jean-Marie, Donald, Andrew, Brian), Josh, Melissa, Ola, Will
Notes
Beta4.0
- Melissa, Jean-Marie, Chris have a few remaining tickets
- Windows seems to be on schedule.
- Colin will test and give feedback on Windows deploy
- DV threshold: will work for demo but need to think about other stratgies
- Tuesday for packaging.
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Doing it on Windows image with EXE4J
- Try Insight
- Extra build for editor? (Otherwise by hand)
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OMX Data & Negative pixel intensities
- issue only applies to 32bit float issues
- shrinks positive from 64k to 32k to -32k. possibly issues. @Jason checks data.
- possibly needs other adjustments somewhere: slider?
- wait for 3.1? (wait for 32bit switch)
- if just a two line change and it works, give it a try
- important in other domains (dicom, EM-tomography) to accept non-positive values
- @Chris gives Melissa DV file with altered header for testing
- @Brian tests the broken dicoms
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Few importer format issues (Leica, xcde, ND2 white images).
- Would be good for Tuesday
- No 4.0.2 - Push to 4.1
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Feedback
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Naming of leica files? (Paulo)
- Creating an image folder?
- Originally a request to keep the original file names
- Now users who don't change their file names have many image with the same name
- Perhaps use image full path on import?
- Was: [Full path]
- Possibly don't give user a choice of dataset, just project?
- @Brian writes to list and discuss (possibly with GUI mockups)
- Curtis: should bioformats create a dataset in the format? * Giving users data management choice. * If there's a concrete choice, it'd be fine. * Vendors will probably start doing this more often. (file as DB) * So should it be bioformats role to say "there's a field 'X', ..." * Traditionally PDI was user driven. Possibly use > * Need construct to differentiate between from user or file. * Using image-image links? * Series name is often the same as the experiment. Or file as patient study <li>
- Regex/etc. in DB for how you name things based on field 'Y'
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Import in general
- Regex in file filter ?
- Users want things to be as fast as possible
- No choice if multiple images chosen?
- Button: "Ask me again?"
- @ Leads to preferences issue! 4.2 Discuss in Paris. * New table with user_id, format_type, colA, colB, colC, ...
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Naming of leica files? (Paulo)
Beta4.1
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SPW
- Need extra metadata coming from bio-formats, without modifying the model
- Adding 4 methods to be filled out in the InCELL reader (origin, sequence, naming scheme)
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Other big user stories
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ROI
- lots of mapping into each languages
- hibernate-spatial requires PostGIS
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OpenGL
- can no longer just write on top of the viewer (its a window onto the hardware)
- working on it while J-M is gone?
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Movies
- Chris spent some time on exporting movies
- Doesn't need client to start
- Gateway, ImageJ, & FS over samba via IM
- @ The big stories need to get broken up soon to make them manageable
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ROI
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All not in 4.1 into Future
- Coming up to Paris we point people at Future
- @ Discuss in Paris
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SPW
ROI in XML Schema
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Why is the naming scheme the way it is? (capitalization)
- Matching SVG is good. Exporting to illustrator, etc.
- If we are breaking anyway, then don't have to worry about it but have a XSLT.
- Trying to get something other than measurement tool for use cases
- @ Discuss in Paris
- If you have to change, change early.
- Supported as is with custom methods to start parsing values from files (OIF)
- Doing ROIs server-side in 4.1, then the tables will be created
- Slowness of some parsing. Java DOM issue? Possibly rework XSD-FU (also solves ordering issue)
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Q: Anything that isn't representable?
- Arrows, SCALE BARS, color bars, text overlays (w/ rendering details)
- origin of text as one of the overlay attributes
- have seen: bounding box + font + color (undisplayed rectangle with text?)
- trying to break SVG as little as possible. (cF. bitmask)
- angled rectangles? (cF. affine transform attribute)
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Why is the naming scheme the way it is? (capitalization)