Open Microscopy Environment

We are using a Molecular Devices ImageXpress Ultra, Confocal High Content Screening System . The software, metaxpress outputs the images in a single directory as tif files and writes all metadata to a Microsoft SQL database.

I was wondering what the best way would be to import these images into Omero while doing the following

1. maintain as much metadata as possible (metadata extraction from MSSql and transfer to postgres and or OME-XML?)
2. maintain the wave length information for each file (w1 -> wavelength 1, etc...), Z stack information (where applicable)
3. Maintain the well/plate organization and allowing the concatination of multiple images taken from a single well.

Any help or pointers on how to get started on this would be greatly appreciated.

Hi,

The best thing to do would be to send a few example datasets, so that full support for this format can be added to Bio-Formats and OMERO. If possible, it also helps if you can provide a brief description of each dataset, e.g. how many wells/fields/channels, the expected name of the plate(s), and the expected channel wavelengths.

In case you need somewhere to put files, I will send you our FTP server details privately.

Regards,
-Melissa

Hi Melissa,
thanks for the offer to help on importing metaXpress data into Omero. Unfortunately I cannot provide a dataset as it seems to be impossible to export data from metaXpress in a meaningful way:

• All metdata concerning the acquisition, plate information, images, etc is stored in a MsSQL DB
• All images are raw tif file (16 bit) with no extra metadata

I can also export a dataset to the same 16 bit tif files and metaXpress will in this case generate a HTD file to go along with the dataset. Omero does not know what to do with it as it tries to import it as an image which fails:

Code: Select all

> [0] Importing "/Users/mmm/Desktop/array642 2x bin/20101124  big head LamA 2 bin2x2_Plate_642/TimePoint_1/20101124  big head LamA 2 bin2x2.HTD"
> [0] Loading image "20101124  big head LamA 2 bin2x2.HTD"...
> [0] Failure importing.


The TIF images get imported just fine but no metadata does go along with it. The HTD file looks like this:

Code: Select all

"HTSInfoFile", Version 1.0
"Description", "XPO1ÇÅÇÅÇÅoverlaid with ATCC HelaÇÅfor 48 hoursÇÅÇÅ1 x confluent T25 around three million cells per arrayÇÅÇÅstandard fix and label methodsÇÅÇÅ1 to 500 pyÇÅ1 to 2000 2y"
"PlateType", 8
"TimePoints", 1
"XWells", 36
"YWells", 13
"WellsSelection1", TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE
"WellsSelection2", TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE
"WellsSelection3", TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE
"WellsSelection4", TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE
"WellsSelection5", TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE
"WellsSelection6", TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE
"WellsSelection7", TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE
"WellsSelection8", TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE
"WellsSelection9", TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE
"WellsSelection10", TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE
"WellsSelection11", TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE
"WellsSelection12", TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE
"WellsSelection13", TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE
"Sites", FALSE
"XSites", 1
"YSites", 1
"Waves", FALSE
"NWavelengths", 1
"WaveName1", "TEXAS RED"
"WaveCollect1", 1
"UniquePlateIdentifier", "0e9c941b-ce9e-4d16-ae2c-1465ab1f8656"
"EndFile"


The amount of metadata in the HTD is negligible but I have the hope, that once omero can be convinced to recognize the file I can add more fields to it.

Unless we find a way to pimp the HTD file it seems that there is no way around to hack the omero importer to open up a connection to the msSQL database to get the needed metadata and then combine that information with the image files. It would be much easier though to write a little script to create a valid and more meaningful HTD file even if we have to modify the importer to recognize the extra fields we would like to add.
Is there a sample HTD file that is recognized by Omero that I can download to be used a a template? Is the import of HTD plus images supported in the first place?

Any further help on this would be greatly appreciated.

Cheers Juergen