OMERO Workshop: Review Wiki

[ajpatterson]

Review the wiki pages linked off:

​http://dmbi.nbi.bbsrc.ac.uk/index.php/OMERO_in_action

Check your email for the OmeroUser? login details to allow editing. (14 March 2011, 19:40 from Jason)

The pages to review are:

• Getting Data In (OMERO.importer, dropbox, bioformats) - Will
• Managing your data (Tags, Sharing, File Attachements, Searches) - Will
• Viewing your data (Viewing / Rendering - 5D image viewer, channels, rendering settings, apply rendering settings across many images) - Scott
• Remote Web access (OMERO.web) - Andrew
• Getting Data Out (OME-TIFF, Figure export, Tag to spreadsheet) - Scott
• Measuring with OMERO (ROIs, Scripts) - ?
• Accessing data using OMERO (CLI, APIs, Scripts, Matlab, Analysis, imageJ, bioformats, cell profiler, volviewer) -?
• Experimental Metadata capture. (OMERO.editor / OME-XML) - Will & Andrew
• Where to next
• The OMERO Community (Forums, Mailing list, Wiki) - Andrew

[wmoore]

I've read all the Day 1 workshop pages...

Made small changes to OMERO in action, adding some lines to a couple of pages:

Managing Data:

• "When deleting a Project or Dataset, you will have the choice of whether to delete it's contents. If you decide not to, the contents will become orphaned."
• "Orphaned Datasets will appear in the hierarchy tree. All images (including orphans) can be found under the 'Images' tab below the hierarchy tab."
• "When you have edited these fields, you can save the change using the 'Save' icon in the tool bar at the top of the metadata pane."
• "Changes to rating should be saved with the 'Save' icon in the tool bar."
• "You can also add a tag to a tag set by right-clicking on the tag set."

Viewing Data:

• "You can specify the range of Z-sections projected using the Z-sliders to the left of the image."

Data Out:

• The "Export a report" functionality is really about exporting Tag data on selected images, giving the number of tags on each image etc. This is not mentioned or demonstrated in the instructions.

Time allowing, you may want to include instructions on:

• filtering of images in the center panel, E.g. by rating, tag, name.
• Collaborative tagging, comments etc.

[saloynton]

I have made the changes in:

Viewing your data:

The Image Viewer Toolbar Display metadata control.

• Compression. The selection of the compression level is used to adjust the image quality. This should be taken into account for when using OMERO over a slower internet connection. (Note: change required to image.)

• Minor Correction: You can now close the image viewer and open a different image by double clicking it in the workspace. You should see that the icon is enabled for this image. Press the paste icon to apply the render settings on the image.

Getting Data Out:

I have inserted an extra exercise for Export to OME-TIFF

Export to OME-TIFF

• Exercise 2 - Open the OME-TIFF image with imageJ.

[wmoore]

E-mail response from Jerome to my edits above

Thanks Will, very much appreciated...

I'll sort out the data out / export section, was kind of testing as writing, so this is not the clearest of sections yet...
Also had issues with the publishing scripts due to my 4.2.1 version but upgraded to 4.2.2 and they are working now, so need to document that.

> - Filtering of images in the center panel, E.g. by rating, tag, name.  
Yup that needs adding, but wasn't sure where as I don't want to tell people about filtering before introducing rating, tags etc... 
If you have any suggestions that would be great.

>- Collaborative tagging, comments etc. This functionality almost makes the web "sharing" feature redundant. 
K will have a go at that and document.

Thanks again for the edits!

[ajpatterson]

Current pages have been reviewed - move to next sprint and further pages will be reviewed as they are added by Jerome.

[jburel]

Moved from sprint 2011-03-24 (8)