About
This is the home of the SLASH project. SLASH stands for "Scalable system for Large data Analysis and Segmentation utilizing a Hybrid approach" (yes it's a mouthful) and represents the name of a 3 year grant we submitted in Oct 2010, and were awarded May 2011. This is a joint grant shared between the The National Center for Microscopy and Imaging Research (NCMIR) at the University of California, San Diego (UCSD) and The Scientific Computing and Imaging Institute (SCI) at the University of Utah. The aim of the grant is to: "to couple novel automatic algorithms with highly scalable tools for collaboratively refining segmentations" with SCI heading the charge for the development of novel automated algorithms, and NCMIR performing data collection and work on collaborative segmentation system. SLASH is a project spawned from the "NeuroSeg" group, and we still use a "neuroseg" e-mail list (neuralseg@sci.utah.edu), so it's easy to get the two terms confused. To learn more about this grant contact Rick Giuly.
SLASH Development and Design Milestones
Meetings:
- In accordance with the grant, meetings are held bi-weekly - typically every second Wednesday at 2:30 in the NCMIR conference room, teleconference to Utah.
- Meeting Minutes - here we try and maintain minutes from any important meetings.
SLASH Module List:
- WIB Client
- WBC Mobile Client
- CellSculpt Client
- WIB Image Server
- Collaborative Management Middleware
- Resource Manager
- CCDB
Converter List:
- IMOD binary model -> CCDB Annotation XML, (program type?) (Andrew)
- CCDB Annotation XML -> IMOD binary model, (program type?) (Andrew)
- CCDB Annotation XML -> Multi-Label Volume, command line tool (Steve Lamont)
- Multi-Label Volume -> CCDB Annotation XML, command line tool (Liz?)
- Single-Label Volume -> XML contours, libcontour command line tool (Steve Lamont)
- ftp://ftpuser:PASSWORD@ftp.ncmir.ucsd.edu/spl/RPMS/sconvert-1.0.0-1.x86_64.rpm
- ftp://ftpuser:PASSWORD@ftp.ncmir.ucsd.edu/spl/RPMS/extractor-1.0.0-1.x86_64.rpm
Developer Area:
- SLASH wiki pages:
- SLASH - Architecture - explains how components of SLASH fit together.
- SLASH - Segmentation pipeline sequence diagram - represent chain of events during segmentation process.
- SLASH - Use Cases - includes original use cases from grant, and more should be added.
- SLASH - Development and Design Milestones -
- CCDB Annotation XML - outlines the structure of the XML we should all use for saving and loading contours - including load/save to the CCDB.
- PDF documents:
- Segmentation System Diagram and Requirements (pdf) - Rick's diagram showing how part interact
- Segmentation System Module Diagram -
- Module documentation:
- CellSculpt - Architecture - includes concept diagram and shows how CellSculpt interfaces with the CCDB.
- CellSculpt - Backend - shows how CellSculpt interfaces with slash tables in CCDB. See also: "Frontend" for class diagrams.
- WIB Image Manager - Steve Lamont's server used by WIB and CellSculpt to deliver image tiles.
- WBC Mobile Technical Details - Rich Stoner's project allowing viewing and tracing data on iPhone and iPad.
