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User Story #2847 (closed)

Opened 9 years ago

Closed 8 years ago

Cecog integration

Reported by:	jamoore	Owned by:
Priority:	minor	Milestone:	Unscheduled
Component:	Scripting	Keywords:	n.a.
Cc:	wmoore, michael.held@…	Story Points:	n.a.
Sprint:	n.a.	Importance:	n.a.
Total Remaining Time:	n.a.	Estimated Remaining Time:	n.a.

Description

For BII2010, some initial integration work will be invested into allowing execution of https://trac.cellcognition.org/ via OmeroScripts.

References

Change History (18)

comment:1 Changed 9 years ago by jmoore

(In [7995]) Initial Run_Cecog.py as well as refactoring (See #2847)

comment:2 Changed 9 years ago by jmoore

(In [7999]) Fixing import issues with cecog.py (See #2847)

comment:3 Changed 9 years ago by wmoore

(In [8003]) split_image() method for downloading Cecog files. See #2847

comment:4 Changed 9 years ago by wmoore

(In [8004]) Final tweeks to Run_Cecog.py to use split_images(). See #2847

comment:5 Changed 9 years ago by jmoore

(In [8016]) Duplicating to Run_Cecog_4.0.py which now works (See #2847)

comment:6 Changed 9 years ago by jmoore

(In [8017]) Better configuration for Run_Cecog_4.0. Failing on analysis (See #2847)

comment:7 Changed 9 years ago by wmoore

(In [8018]) Cecog Demo Working! Still with some hard-coded values "0037" etc. Missed the fact that Run_Cecog_4.0.py existed, so was only using Run_Cecog_4.1.py (with Cecog 4.0.7).
Added methods to script_util since I didn't know how to call CLI! See #2847

comment:8 Changed 9 years ago by jmoore

(In [8031]) Running version of Run_Cecog for 1.0 and various refactorings (See #2847)

comment:9 Changed 9 years ago by jmoore

(In [8032]) Renaming to the appropriate Cecog 1.0 (See #2847)

comment:10 Changed 9 years ago by jmoore

(In [8033]) Storing result images back in original dataset (See #2847)

comment:11 Changed 9 years ago by jmoore

(In [8034]) Adding rois for cecog data (See #2847)

comment:12 Changed 9 years ago by jmoore

(In [8035]) Multiple ROIs per shapes and a file attachment with the object details (See #2847)

This also works around insight:ticket:1596 in which rois without a Z
set are not shown on all planes.

comment:13 Changed 9 years ago by jmoore

(In [8118]) Minor cosmetic fixes for Run_Cecog_1.0.py (See #2847)

comment:14 Changed 9 years ago by jmoore

(In [8119]) Disabling Run_Cecog_1.0.py for release (See #2847)

comment:15 Changed 9 years ago by jmoore

Milestone changed from OMERO-Beta4.2.1 to Unscheduled

After disabling cecog from the default install, pushing this to unscheduled.

comment:16 Changed 9 years ago by wmoore

(In [8603]) Fix bug in script_utils.py for downloading image as Cecog tiffs. See #2847

comment:17 Changed 9 years ago by wmoore

(In [8938/omero]) Cecog export script. See #2847

comment:18 Changed 8 years ago by jburel

Resolution set to wontfix
Status changed from new to closed

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