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Task #3534 (closed)

Opened 10 years ago

Closed 10 years ago

Last modified 10 years ago

Review of Big Image Workflow with Thomas

Reported by: saloynton Owned by: saloynton
Priority: minor Milestone: OMERO-Beta4.3
Component: Usability Version: n.a.
Keywords: n.a. Cc: jburel
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: 2010-12-23 (2)

Description (last modified by saloynton)

Meeting with a scientist the week beginning the 29th of Nov, date to be confirmed by scientist. The purpose is to take screenshots and document the problems as the as he works with big images in softworks.

UPDATED: Thomas's work has been effected by the snow and so I will be contacted the week beginning of the 6th of December for a re-arranged meeting.

UPDATED: Spoke with Thomas on 8th Dec and microscope session arranged for 16th Dec.

UPDATED: Meeting Notes 16th Dec

The steps taken by Thomas in softworks when viewing his images:

Rendered image > quick projection > Image Stitching (if required) > Volume viewer

(Thomas conducts several of these steps on the computers that have sufficient processing power to work with the large images he creates.)

The type of image Thomas is viewing determines the step of image stitching. The larger germ line images are stitched at this point in the workflow. The images we were viewing for the demo were cells and so were not stitched. The work conducted in the volume viewer sets out the required information values for the image. This covers options such as viewing parameters, movie options, and wavelength scaling. (See screenshot 1 for details)

During this process Thomas highlighted the issue of having to manage and deal with the large images require a large amount of his time. From the start of the start of the process of de-convolution to the projection of a germ line every single image that will typically have 90 – 120 stacks, in addition the images are stitched together with several panels.

The zooming process for softworks was performed either with the zoom bar on screen or with the mouse roller wheel. This was comparable to experience of gmaps. (See annotated screenshot 2 for details). The only other notable detail in the viewer was the use of the scale bar at the bottom of the image.

The remaining discussion with Thomas focused upon his analysis work. The analysis Thomas had been currently working with required him marking out points on the images to calculate the average signal intensity. He also needs to be able to go on to calculate the average intensity around the cell membrane without the bias. Thomas mentioned the new version of emaris is able to do this calculation. (See annotated screenshot 2 for details)

Follow up actions: Keep Thomas updated on continuing work scheduled for week beginning 7th Feb 2011, possibility to get more screenshots if require.

Change History (11)

comment:1 Changed 10 years ago by saloynton

  • Owner set to saloynton

comment:2 Changed 10 years ago by saloynton

  • Status changed from new to assigned

comment:3 Changed 10 years ago by saloynton

  • Owner saloynton deleted
  • Status changed from assigned to new

comment:4 Changed 10 years ago by saloynton

  • Description modified (diff)
  • Owner set to saloynton
  • Summary changed from Review of Big Image Workflow to Review of Big Image Workflow with Thomas

comment:5 Changed 10 years ago by saloynton

  • Description modified (diff)

comment:6 Changed 10 years ago by jburel

  • Sprint changed from 2010-12-09 (21) to 2010-12-23 (22)

Moved from sprint 2010-12-09 (21)

comment:7 Changed 10 years ago by saloynton

  • Status changed from new to accepted

comment:8 Changed 10 years ago by saloynton

  • Description modified (diff)

comment:9 Changed 10 years ago by saloynton

  • Description modified (diff)

comment:10 Changed 10 years ago by saloynton

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

comment:11 Changed 10 years ago by saloynton

  • Description modified (diff)
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