Integrating InCell instruments into open-microscopy

[foisys]

Hi,

My lab is building a high throughput screening platform built around two InCell microscopes (a 2000 and a 6000) which I am working to integrate using the IN Cell Miner Server/Client + IN Cell Investigator suite. I am finding the whole process highly troublesome and irritating, the requirement for Oracle being a major pain.

Could we consider OMERO as a possible alternative/complement to this platform some time in the future? I am a big proponent of open source solutions for bio-informatics in and around here and have used OMERO before for low-throughput data very much to my satisfaction

Any inputs appreciated

Sylvain Foisy, Ph. D.
Project Manager Bio-informatics
Montreal Heart Institute
Montreal, Qc
CANADA

[rleigh]

Hi,

In Bio-Formats (used by OMERO for reading image data), we support reading of the InCell1000 and InCell3000 file formats. The 2000 format is the same as the 1000. I'm not sure about the 6000 format; I would suggest testing to see if this the same as the 3000.

For the InCell1000/2000, we support reading plates into OMERO. For the 3000 (and I suspect also the 6000), the plate metadata is, as far as I'm aware, stored in the Oracle database, making it impossible (at the present time) to import the data into a plate; it is possible to import the individual images, however. With further development, it might be possible to also connect to the Oracle database and retrieve the data, but we do not do this at present. In general, we can't support connecting to Oracle databases.

While OMERO can certainly complement the InCell software for storing of the data post-acquisition, it certainly won't be able to replace the acquisition software. If the acquisition software depends upon the Oracle database to function, I doubt we can replace the use of Oracle entirely; though you may be able to move the data out into OMERO after the acquisition is complete.

So for the 2000 system, we should be able to import the data without issues.
For the 6000 series data, I would suggest taking a look and seeing if it's importable. You can always send us a sample dataset and we can take a closer look into it as well. We may be able to update one of the InCell readers to support it if it's not completely dependent upon Oracle.


Kind regards,
Roger Leigh

[foisys]

Hi,

Thanks for the feedback I am taking note of the relationship between the various generations of equipment. Right now the microscopes are working as standalones, not yet connected to the IN Cell Miner Server system... It could be interesting to try to create an OMERO server to try to connect the instruments to it. You are quite right that trying to have the two systems (IN Cell Miner and OMERO) connecting to each other would be a challenge...

As soon as we get some 6000 imagery, I'll send them over for analysis.

Thanks for the inputs

Sylvain