Open Microscopy Environment

Hi -

My apologies in advance if this isn't the correct forum for this post.

We are testing the feasibility of using inplace import (ln_s, symbolic link) feature of the OMERO.Server for screening images generated by CellVoyager CV7000S high-throughput imaging microscope.

CV7000S saves individual TIF images for each XY, Z, T, Channel/Wavelength, and Field as well as several accompanying XML files (.mrf, .mlf, .mes, and .wpi). These XML files contain metadata about the experiment, plate, well and field position, etc. You can get a brief overview of the file naming convention here:

https://github.com/stoeter/Fiji-Tools-for-HCS/wiki/Yokogawa-CV7000-file-names

As a starting point, we are using the docker recipe files from OME's DockerHUB repos (omero-server/latest, omero-web-standalone).

We are able to do an inplace import of the a folder containing all the images (and metadata files) using something like this:

Code: Select all

$OMERO import -s localhost -p 4064 -g $LABNAME -u $USER_USERNAME -w $USER_USERNAME -- --transfer=ln_s $IMPORT_PATH  -T "regex:+name:^.*${USERPATH}/(?<Container1>[^/]*)/.*"


The import command ignores XML files (.mrf, .mlf, .wpi) but successfully imports all .tifs in the folder into a Dataset in the OMERO.SERVER.



Is it possible to import the folder from CV7000S into a plate layout (Screen Tab in omero.insight)? We would like import and display the images as IDR's Spatial Grid View.

[url]
https://github.com/openmicroscopy/openm ... -258405216
[/url]

We are looking at the "Dataset_to_Plate.py" script as a starting point to export the "Dataset" to "Screen" but if there is a more direct way to accomplish this it would be wonderful.



Thanks,

Prabhakar Gudla

Hi Prabhakar,

Thanks for getting in touch with us. At the moment, Bio-Formats 5.8.2 only supports datasets generated by the Yokogawa CV1000 imaging systems [1]. Your CV7000S datasets are currently detected as individual TIFF files and imported as single images into OMERO. In order to import these files directly as plates onto OMERO, a new reader needs to be developed that detects these datasets as HCS data.

Yokogawa has recently partnered with Glencoe Software to integrate their imaging data into OMERO Plus [2]. So far there has been no public request to port this work back to the open-source. It would be great to know if carrying out this effort would be of general interest for the community before we assess the feasibility on our side.

From the open-source side, assuming the backporting is possible, we would still need representative sample datasets of the CV7000 file format, ideally publicly shareable under CC-BY license. These sample files allow us to test non-regressions of our readers and ensure the readability of imaging data. Would you have such data that could be shared with us?

Best,
Sebastien

[1] https://docs.openmicroscopy.org/bio-for ... yager.html
[2] https://glencoesoftware.com/2018-03-01- ... arian.html

Hi Sebastien,

Thanks for your prompt response and useful pointers.

Yes, we are aware of Yokogawa's CellLibrarian but we're looking for open-source solution. We are actually working on something similar to IDR with VAE (virtual environment for analysis). So image management and visualization is just one aspect of it.

I think we should be able to generate a dataset and release it under CC-YB. We probably already have some datasets but can design acquisition to cover typical usage.

What is the best way to upload the dataset?

Thanks,

Prabhakar (Reddy) Gudla

Hi,

To keep you updated, we started discussing the backporting of the Bio-Formats fixes used in Yokogawa's CellLibrarian in this reference card. As you can see, collecting additional samples of acquisition systems more recent than CV7000 would be really helpful as we are considering the scope of this work.

In terms of upload, it depends on how big your datasets are. For datasets smaller than 2GB, you can upload them directly at http://qa.openmicroscopy.org.uk/qa/upload/ e.g. after zipping them. For datasets of bigger sizes, we can provide you private information about an FTP server to upload them. Please let us know what your preferred mechanism would be.

Best,
Sebastien

Sebastien -

Great! Thanks a bunch for moving on this request.

We will look into the preparing the datasets. I'll probably send you a PM with details.

Thanks,

Prabhakar