2010-02-16 Tuesday Meeting
Attending:
Agenda
Remember: Agenda must be complete (with estimated times) on the day before the meeting. Any additions after that must go at the bottom (AOCB)
-
Matters Arising (<10 mins)
- Everyone: review the use case list on RoiStorage wiki
-
@For Tuesday, Scott and Josh get a page up with the summary
- summary - Needs some more review, but largely collated.
- Data Storage: Donald's presentation (45 mins)
-
AOCB (<5 mins)
- Zurich?
- Estimates?
- BMVA Meeting on Microscopy Image Analysis for Biomedical Applications?
Notes
Matters arising (15-15:15)
- Reviewing ROI use cases, made more clear by the presentation
-
process-summary
- Review for Thursday? @Yes
- some are softer requirements; what should happen?
- avoiding "it's not written I won't do it"
-
bug this morning
- trying to use OMERO for EM.
- possibly interesting. already getting feedback.
- @Jason writes to Agilo for Thursday
- @Domain registration
- About pages
Data storage presentation (15:15-15:45)
-
intro
- coming from roi/roi storage mini-group
- were discussing mechanisms for storing ROIs
- planned to investigate alternatives
-
"what an roi?" is still a bit open (influences storage)
- if we want it to be multiple things, then we need to be able to store both
- Chris: we don't have all of the things defined here (e.g. annotated links)
- Jason: phrasing? Geometry includes time. Subset of the dimensions.
-
Use Cases
- user-created/hcs/external/templates
- "External?" Anything not written by us (maybe scripting as well)
- different use cases for each type
-
Current storage
- Pytables doesn't like hetereogenous data, issue with tagging
- Database linking issues & annotation table size
-
Alternative storage
- key-value stores require building your own query structure
-
summary
- mongodb & document db is Donald's favorite
- bigtables-cousins would be great for purely measurements
- but we want to do more relational work
-
normalization
- do we actually use it as a relational db?
- at the import stage: objective settings, SPW, ...
- making our life difficult, since we don't make any use of RDB
-
intro
Data storage Q&A (15:45-16:!7)
-
document store
- use for various things, not just ROIs
- ROI/ROI-LINKS: doesn't rule it out (not for free)
-
transitional phase is an issue
- do we want to work toward a single storage mechanism?
- do we use the best storage mechanism for a particular type?
- what's the scope? (4.2?)
- which project would show the utility?
-
Chris:
- don't currently utilize the ROI object in db correctly
- InCell you'd tag every ROI with correct tag (cell/nucleus)
- ROI as an object is un-utilized
- getting us (and our users) out of a situation.
- Donald: currently blocked. make this decision rather than later.
-
document store
AOCB
- @Update estimates by EOF on Wednesday on your work plans
- @Decide who goes to meetings by Thursday