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User Story #1739 (closed)

Opened 11 years ago

Closed 11 years ago

Last modified 10 years ago

EM software integrated with OMERO

Reported by: wmoore Owned by: wmoore
Priority: major Milestone: Unscheduled
Component: General Keywords: n.a.
Cc: Story Points: n.a.
Sprint: n.a. Importance: n.a.
Total Remaining Time: n.a. Estimated Remaining Time: n.a.

Description (last modified by wmoore)

Investigate the options for using OMERO as the image repository for single particle analysis work-flows. This is a very ambitious task to do properly, and will probably require significant help from developers of the single-particle software. Current aim is to see whether a proof of principle is possible.

Example workflows:

Importantly, EMAN2 is written in Python, and SPIDER has some Python scripts (full bindings in development).

The 2 main options are (as always):

Client-side software

E.g. Have SPIDER or EMAN2 running on the client. Adapt existing scripts to access data on OMERO. Shouldn't be too hard to do with individual scripts using small numbers of images. But when many large images are required, this becomes impracticable.

Server-side software

Use the OMERO scripting service to call Python functions in SPIDER or EMAN installed on the server. Scripts will still have to convert pixel data into the correct file type (temporary data duplication), but won't have to move data over the wire.

EMAN2

Currently EMAN2 is looking like a good option for Python-based processing. Investigating early steps of Single-particle analysis, with server-side scripts called via the scripting service:

These include:

  1. Particle picking boxer.py
  2. Generating particle images from ROIs imagesFromRois.py
  3. CTF estimation and filtering

Attachments (2)

06jul12a_00027gr_00065sq_00009hl_00003enCrop.tiff (8.6 MB) - added by wmoore 11 years ago.
Sample data for testing script
boxer.py (9.8 KB) - added by wmoore 11 years ago.
Script working better now!

Change History (10)

comment:1 Changed 11 years ago by wmoore

  • Description modified (diff)

comment:2 Changed 11 years ago by wmoore

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

This script is a "proof of principle" to demonstrate how Spider and EMAN2 can work with OMERO.
This uses the auto-box functionality of EMAN2, which takes one or more user-defined particle ROIs,
and uses this as the basis for picking additional particles from the image.
In this script, OMERO is used as the source of the image, with the user-defined particles as ROIs on
the server. Spider is used to turn the plane array into a Spider image. The EMAN2 subclasses
use this, with the server ROI(s) to generate additional ROIs which are then saved back to
the server.
The script below is currently implemented as a client-side script, but could easily be
converted into a server-side script, with EMAN2 and Spider installed on the server.

Usage: Import an image (attached below) draw an ROI around a particle(s) with a width and height of 313 pixels. Run the script (need SPIDER and EMAN2 installed). Refresh the ROIs on the image. Should see that additional particles have been picked.

Changed 11 years ago by wmoore

Sample data for testing script

comment:3 Changed 11 years ago by wmoore

r6045 Fixed bug in getting plane2D, to make Tiff from PIL.

Changed 11 years ago by wmoore

Script working better now!

comment:4 Changed 11 years ago by wmoore

  • Description modified (diff)
  • Resolution fixed deleted
  • Status changed from closed to reopened

comment:5 Changed 11 years ago by wmoore

  • Resolution set to duplicate
  • Status changed from reopened to closed

comment:6 Changed 11 years ago by jmoore

(In [8501]) Hard-coding prefix of 5 for OMERO-python-integration (See #1739, #3225)

comment:7 Changed 10 years ago by jmoore <josh@…>

(In [ebfccda1b2540518223f3ead5acae3f97f6b0a0c/ome.git] on branch dev_4_1_custom) Hard-coding prefix of 5 for OMERO-python-integration (See #1739, #3225)

git-svn-id: file:///home/svn/omero/trunk@8501 05709c45-44f0-0310-885b-81a1db45b4a6

comment:8 Changed 10 years ago by jmoore <josh@…>

(In [ebfccda1b2540518223f3ead5acae3f97f6b0a0c/ome.git]on branches 4_1_custom, dev_4_1_custom, josh/4.1-web-backport) Hard-coding prefix of 5 for OMERO-python-integration (See #1739, #3225)

git-svn-id: file:///home/svn/omero/trunk@8501 05709c45-44f0-0310-885b-81a1db45b4a6

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