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Task #10040 (accepted)

Opened 7 years ago

Last modified 4 years ago

Many Channels to 1 Logical Channel

Reported by: wmoore Owned by:
Priority: major Milestone: Unscheduled
Component: Import Version: OMERO-5.2.0
Keywords: n.a. Cc: mlinkert, jamoore, cxallan, jburel
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

I noticed that if you import the mias Plate at

from_skyking/mias/frans/siRNA_PRIM1_03102008

then query the DB (after finding most recent logical channel)

omero=# select * from Channel where logicalchannel = 4451;

...
 5002 |   255 |    0 |         -40 |     0 | 255 |         |      160423 |             |        3 |        3 |    160427 |           4451 |   4401 |      4932 |            1
 5001 |   255 |    0 |         -40 |     0 |   0 |         |      160423 |             |        3 |        3 |    160427 |           4451 |   4401 |      4931 |            0
(32 rows)

you find that ALL the Channels (2 channels * 16 images) are linked to one Logical Channel.

Noticed this when renaming channels #10022.

This has implications if you want to have different names for the 2 channels in each image OR for future DB upgrades where Channel & Logical Channel may be merged.

Should probably ensure Channel : LogicalChannel? is 1:1.

Change History (4)

comment:1 Changed 7 years ago by mlinkert

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

comment:2 Changed 7 years ago by wmoore

  • Resolution fixed deleted
  • Status changed from closed to reopened

Since creating this ticket, I was looking at how it's handled in other Plates I import: I see that for a whole Plate, the number of Logical Channels is equal to the number of Channels in each image. E.g. in this example, an Image from a Plate has 2 Channels and 2 LogicalChannels?:

omero=# select id, logicalchannel from channel where pixels=3901;
  id  | logicalchannel 
------+----------------
 4252 |           4152
 4251 |           4151
(2 rows)

The problem in the data I imported for this ticket is that there is only 1 logical channel for this Plate, even though every image has 2 channels. E.g:

omero=# select id, logicalchannel from channel where pixels=4417;
  id  | logicalchannel 
------+----------------
 5034 |           4452
 5033 |           4452
(2 rows)

There simply needs to be 2 Logical Channels for this plate instead of 1 (from_skyking/mias/frans/siRNA_PRIM1_03102008).

comment:3 Changed 4 years ago by jamoore

  • Milestone changed from 5.x to Unscheduled

comment:4 Changed 4 years ago by mlinkert

  • Owner mlinkert deleted
  • Status changed from reopened to accepted
  • Version set to OMERO-5.2.0

This needs to be checked again to verify that it's still a problem, but I'd expect it to require a fix in OMERO and not Bio-Formats.

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