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Requirement #1950 (closed)

Opened 11 years ago

Closed 10 years ago

Big Images

Reported by: wmoore Owned by: jamoore
Priority: critical Milestone: OMERO-Beta4.3
Component: General Keywords: n.a.
Cc: atarkowska, jburel, jrswedlow Business Value: n.a.
Total Story Points: n.a. Roif: n.a.
Mandatory Story Points: n.a.

Description (last modified by wmoore)

Maybe we've got this somewhere else, but I can't find it just now, and I need somewhere to put down requirements, thoughts etc.

Big Images is where we have large planes, and is related to 'Tiling' but tiling is a separate issue (different 'Requirement'?).

API wish list for Big Images (one way to start thinking about it):

RawPixelsStore:
 * getPlaneRegion(int z, int c, int t, int x, int y, int width, int height, zoom) 
 * setPlaneRegion(int z, int c, int t, int x, int y, int width, int height)
 * getCubeRegion(x,y,z, w,h,d, zoom)  - see below

RenderingEngine:
 * renderCompressedRegion(PlaneDef p, int x, int y, int width, int height, float zoom)
E.g. zoom = 0.5 to get a region at half normal size. 
 * etc. for other methods. 

EXAMPLE USE CASES:

  • Catmaid is a "google-maps" (with Z) browse and annotation tool for large images that uses an image pyramid from TrakEM2.

http://www.ncbi.nlm.nih.gov/pubmed/19376822
http://fly.mpi-cbg.de/~saalfeld/catmaid/
Would be nice if we can support clients like this, either by generating an entire jpeg pyramid when the image is imported or opened, or making each tile on the fly as required?

  • Open Astex Viewer, as an applet runs out of memory when rendering a cube over 160 x 160 x 160 (approx). To view larger volumes in 3D, we scale down in 3D. Currently do this in Ingvar's java code and save as a sub-sampled mrc.map, but might be nice to do on the server. Not sure what the API would look like, but I guess it would be: getCubeRegion(x,y,z, w,h,d, zoom).
  • The pre-calculated solutions (GMaps, CATMAID) are fine, and very powerful. Our approach has been to allow re-scaling of images, and this is critical for viewing data.

WIDER API IMPLICATIONS:

If we're going to be revamping the ROI to access pixel data that is not necessarily adjacent on disk...? Then there are a bunch of other methods that might be nice:

  • getXslice(theX, theC, theT)
  • getYslice(theY, theC, theT)
  • X & Y projections?


Change History (11)

comment:1 Changed 11 years ago by jmoore

  • Milestone changed from Unscheduled to OMERO-Beta4.2

comment:2 Changed 11 years ago by cxallan

  • Milestone changed from OMERO-Beta4.2 to Unscheduled

comment:3 Changed 11 years ago by jmoore

  • Priority changed from minor to critical

Prioritizing for 4.2+

comment:4 Changed 10 years ago by wmoore

  • Description modified (diff)

comment:5 Changed 10 years ago by wmoore

  • Description modified (diff)

comment:6 Changed 10 years ago by atarkowska

  • Cc atarkowska added

comment:7 Changed 10 years ago by jburel

  • Cc jburel added

comment:8 Changed 10 years ago by jrswedlow

  • Cc jrswedlow added
  • Description modified (diff)

comment:9 Changed 10 years ago by jburel

  • Milestone changed from Unscheduled to OMERO-Beta4.3

comment:10 Changed 10 years ago by wmoore

  • Description modified (diff)

comment:11 Changed 10 years ago by jmoore

  • Component set to General
  • Resolution set to fixed
  • Status changed from new to closed

All stories closed or moved to #5927. This phase 2 includes issues like caching and the measurement tool.

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