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Task #11102 (new)

Opened 11 years ago

Last modified 8 years ago

BUG: Undetected contrast setting in EM DVs

Reported by: rkferguson Owned by: jburel
Priority: major Milestone: Unscheduled
Component: Insight Version: n.a.
Keywords: n.a. Cc:
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description (last modified by rkferguson)

This issue was brought up by Helio during the Oxford site visit and data has been uploaded to QA by Douglas.

EM images:

  • contrast is critical
  • currently appears to be giving full range no matter what
  • histogram/curve usually quite narrow and steep and skewed to middle or right
  • seems to be bug with trying to change range on slider
  • either
    • just does not respond - hangs effectively
    • has no appreciable effect
    • takes ages to re-render


The contrasting settings which are embedded in the image are ignored. I have attached the original image and then one contrasted (badly, but noticeably) to demonstrate the difference. If you open these in softworx they will appear differently, but if you import them into OMERO then the contrasted settings are ignored.

Doing this contrasting in softworx is a step the users are doing anyway, so it's very annoying for them to have to duplicate this work. Particularly as contrasting in softworx is much nicer than the OMERO tools.

Also reports problems with some metadata not being picked up from EM data files

Example files are in QA:

Another issue related to EM data that Helio brought up:

EM produces massive images

  • huge problems viewing them at single resolution
  • would be helpful to have 5 steps (5 a guess but probably ideal) of resolution automatically generated to allow overview and drilling down to increasing detail
  • or have an option that it it is going to take too long then elect not to generate pyramids

and with MRC data Helio uses:

Captures images as MRC files but then reconstructs them as tomograms and 3D views

  • has to be done outside OMERO
  • extension name is then changed to .rec but the data is effectively still .mrc and even identified as this in file type, but they will not import into OMERO

Change History (3)

comment:1 Changed 11 years ago by jburel

  • Summary changed from BU: Undetected contrast setting in EM DVs to BUG: Undetected contrast setting in EM DVs

comment:2 Changed 11 years ago by rkferguson

  • Description modified (diff)

comment:3 Changed 8 years ago by jamoore

  • Milestone changed from 5.x to Unscheduled
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