Warning: Can't synchronize with repository "(default)" (/home/git/ome.git does not appear to be a Git repository.). Look in the Trac log for more information.
Notice: In order to edit this ticket you need to be either: a Product Owner, The owner or the reporter of the ticket, or, in case of a Task not yet assigned, a team_member"

User Story #10230 (closed)

Opened 11 years ago

Closed 11 years ago

Create WND-CHRM demo with existing OMERO codebase

Reported by: spli Owned by: spli
Priority: major Milestone: OMERO-4.4.7
Component: Scripting Keywords: n.a.
Cc: analysis@… Story Points: n.a.
Sprint: 2013-03-12 (6)) Importance: n.a.
Total Remaining Time: 0.0d Estimated Remaining Time: n.a.

Description (last modified by spli)

A feasibility study: can WND-CHRM be added to OMERO with minimal server-side changes? It won't be pretty, but attempting this should highlight areas which are problematic, and means we're not purely working with hypothetical requirements.

Rough outline:

  • Store features in OMERO.tables array columns
  • Label training images using annotations in the database, or screen-style bulk-annotations
  • One script to calculate features from images in a dataset
  • One training script to create a classifier
  • One prediction script to run the classifier

Updated: It roughly works, so the plan is to demo this at the PI meeting 28 February-01 March 2013 after the referenced tasks are done.

Attachments (9)

1-training_set_cat.png (350.6 KB) - added by spli 11 years ago.
2-training_set_hedgehog.png (374.4 KB) - added by spli 11 years ago.
3-training_set_feature_extraction.png (280.0 KB) - added by spli 11 years ago.
4-training_set_build_classifier.png (277.1 KB) - added by spli 11 years ago.
5-test_set.png (462.1 KB) - added by spli 11 years ago.
6-test_set_feature_extraction.png (384.1 KB) - added by spli 11 years ago.
7-test_set_predict.png (311.7 KB) - added by spli 11 years ago.
8-test_set_cat_predictions.png (345.2 KB) - added by spli 11 years ago.
9-test_set_hedgehog_predictions.png (364.4 KB) - added by spli 11 years ago.

Change History (12)

comment:1 Changed 11 years ago by spli

  • Description modified (diff)
  • Status changed from new to accepted
  • Summary changed from Attempt to use WND-CHRM with existing OMERO codebase to Create WND-CHRM demo with existing OMERO codebase

comment:2 Changed 11 years ago by jburel

  • Sprint changed from 2013-02-12 (5) to 2013-03-12 (6))

Moved from sprint 2013-02-12 (5)

Changed 11 years ago by spli

Changed 11 years ago by spli

Changed 11 years ago by spli

Changed 11 years ago by spli

Changed 11 years ago by spli

Changed 11 years ago by spli

Changed 11 years ago by spli

Changed 11 years ago by spli

Changed 11 years ago by spli

comment:3 Changed 11 years ago by spli

  • Resolution set to fixed
  • Status changed from accepted to closed
Note: See TracTickets for help on using tickets. You may also have a look at Agilo extensions to the ticket.

1.3.13-PRO © 2008-2011 Agilo Software all rights reserved (this page was served in: 0.73470 sec.)

We're Hiring!