Open Microscopy Environment

Dear all,

I couldn't find any post about this, but apologies if this has been asked before:

Using insight 5.1.2, is it possible to covert a TIFF stack that was wrongly detected by the importer to be a time series to a z-stack? And vice-versa? Possibly as a batch?

Or even better: to take a range of time series (that ought to be z stacks) and convert them to a single "image" that contains all data (as the figure represented in the help file: Workflow user guides > viewing data> z-stacks and T-points).

Background: my tif's originate from a custom build microscope, of which the metadata is not supported by bioformats.

thanks in advance!
Maarten

Hi,

You can do this using OMERO_Insight as ImageJ plugin.

1) Open an OMERO Image in ImageJ using the OMEROIJ plugin. The installation and usage instructions are described in the following link,
http://help.openmicroscopy.org/imagej.html
2) The image will now be opened within ImageJ and can be manipulated using the ImageJ image processing options.
3) The trick to switching dimensions : Click on Image-->Properties (in the ImageJ Menu).
4) Switch the Z and T values and click OK. This should switch the image properties in the ImageJ Image Window.
5) Export the image as an ome-tiff (using Bio-Formats Exporter : Plugins-->Bio-Formats--> Bio-Formats Exporter) and reimport the image back into OMERO using insight or by using the OMEROIJ plugin.

We have tested this workflow locally and it works. Please let us know if you find otherwise.
Hope that helps.

Best,
Balaji

Dear Balaji,

thank you for describing your work flow - this definitely works for me (but only using re-import with the standalone OMERO insight client).

I also tried the new 5.1 feature Plugins->OMERO->Save Image(s) to OMERO, which would make your work flow truly round-trip editing, but unfortunately the "Import data" dialog that comes up does not list the image that is open in the current window. After doing some more testing I'll probably post a separate question for that, as the issue it is only partially related.

thanks again,
Maarten

hi Maarten

In order to work using the import option of the imageJ plugin, you will have to open the generated OME-TIFF
We are looking into the problem so we can avoid the export as OME-TIFF step.
We need to check that the image properties have been modified

Thanks

Jmarie