Open Microscopy Environment

Hi,
Can I import an image sequence using either insight or web?
I can do this in Fiji.
Image>Import>Image Sequence
Select one of my DICOM files in the sequence and the whole sequence is loaded in and can be scrolled/driven through in the Fiji viewer.

What do I have to do to achieve the same in OMERO?
When I upload my DICOM files I can only view one at a time.

Have viewed other similar discussions on using pattern files and converting to OME.tif but would appreciate a heads up on the possibilities before I dive in further.
I feel as if I am missing something fundamental but can't see what it is.
Many thanks
Derek

Update on previous.
I import the image sequence into Fiji and then export using the BioFormats exporter to single ome.tif file.
Now I can use insight to import and view the sequence which is what I want.
However, there is no original metadata found under Acquisition.
In an attempt to preserve the original metadata I set the export parameters to write each Z section/Timepoint to a separate file but it just created a set of identical files of the whole sequence.

1. Is the above workflow - importing and exporting to and from Fiji - the best route to follow?
2. How do I preserve the metadata?

Thanks
Derek

Dear Derek

When exporting as OME-TIFF not all metadata will be included in the file.
Using pattern files could be an option but before you embark on a path that might not be the most suitable. Will you be able to share with us sample files so we can recommend the most appropriate solution?
You can submit the files using the following link http://qa.openmicroscopy.org.uk/

Cheers

Jmarie

Hi,
I have uploaded the first 100 dicom files (of a set of 300) to the URL you posted.
under the username: derekeh

Not sure if there is something in the metadata which signals which is the last image of the sequence?

Anyway, I tried the 'combine images' script from within insight as suggested by Sebastien but that didn't work. I tried it on all 300 images and I tried it on the Dataset.

Let me know if you need me to post anything else.

Thanks for your help

Regards
Derek

Hi Derek,

thanks for the files. In order to import a sequence into OMERO you need to create a pattern file to stitch the files together, which is what ImageJ is doing under the hood. See https://docs.openmicroscopy.org/bio-formats/5.9.2/formats/pattern-file.html for details, but if I create the following file:

Code: Select all

Im<1-100>.dcm


Then you will be able to import as you expect. For example, when I inspect that with Bio-Formats `showinf` tool, I see the following metadata:

Code: Select all

Reading metadata
0002,0002 Media Storage SOP Class UID #1: 1.2.840.10008.5.1.4.1.1.2
0002,0003 Media Storage SOP Instance UID #1: 1.2.840.113619.2.55.3.163578213.522.1288596941.842.1
0002,0010 Transfer Syntax UID #1: 1.2.840.10008.1.2.1
0002,0012 Implementation Class UID #1: 1.2.840.113619.6.181
0002,0013 Implementation Version Name #1: AW4_3_05_04_EXT_
0002,0016 Source Application Entity Title #1: ct99
0008,0005 Specific Character Set #1: ISO_IR 100
0008,0008 Image Type #1: ORIGINAL\PRIMARY\AXIAL
0008,0012 Instance Creation Date #1: 20101101
0008,0013 Instance Creation Time #1: 095850
0008,0016 SOP Class UID #1: 1.2.840.10008.5.1.4.1.1.2
...


Cheers,
~Josh