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User Story #10230 (closed)

Opened 7 years ago

Closed 6 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.

References

References:

→ Task (#10365): Use Projects IDs field instead of listing datasets ( Owner: spli Remaining Time: 0 ) → Task (#10367): Define namespaces for WND-CHRM outputs and related files ( Owner: spli Remaining Time: 0 ) → Task (#10366): Consider saving WND-CHRM classifier instead of generating on the fly ( Owner: spli )

Attachments (9)

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

Change History (12)

comment:1 Changed 6 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 6 years ago by jburel

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

Moved from sprint 2013-02-12 (5)

Changed 6 years ago by spli

Attachment 5-test_set.png added

Changed 6 years ago by spli

Attachment 6-test_set_feature_extraction.png added

Changed 6 years ago by spli

Attachment 7-test_set_predict.png added

Changed 6 years ago by spli

Attachment 8-test_set_cat_predictions.png added

Changed 6 years ago by spli

Attachment 9-test_set_hedgehog_predictions.png added

comment:3 Changed 6 years ago by spli

Resolution set to fixed
Status changed from accepted to closed

https://github.com/manics/omero-pychrm/tree/20130228-pi_dev_demo

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