[ome-users] OMERO Import - 2+ tiff files

Tue Nov 27 22:26:56 GMT 2007

Thanks for the reply Curtis.  To clarify the failure part of my message.
I was trying to use OMERO.insight to import a 5D image generated using
ImageJ. (I understand why it failed now)

The future solutions sound interesting (file patterns or graphical
tool).  The CellProfiler tool has a nice way of using regular
expressions to identify channels (out file names are terminated with
color name and then tif extension).

My thought on making sure the tile/frame metadata is loaded properly is
to allow display of multiple images in correct X-Y orientation.

Matt

-----Original Message-----
From: ctrueden.wisc at gmail.com [mailto:ctrueden.wisc at gmail.com] On Behalf
Of Curtis Rueden
Sent: Tuesday, November 27, 2007 4:55 PM
To: Smicker, Matthew PH/US
Cc: ome-users at lists.openmicroscopy.org.uk
Subject: Re: [ome-users] OMERO Import - 2+ tiff files

Hi Matt,

> We are able to export files from a proprietary format into a 
> relatively metadata-free tiff format (unfortunately).  Multiple 
> channels are exported as separate files.  Filenames contain the 
> metadata (channel, well).

First of all, what is your proprietary format? Is it something that you
would like to see added to OMERO in the future?

Second, Bio-Formats, the library that drives the OMERO importer, does
support image series distributed across multiple files as part of its
FileStitcher module. It works by scanning for file naming patterns --
numbers that vary across the otherwise consistent filenames. So if you
have a series of TIFFs that are numbered according to channel as you
say, it should be possible in theory for OMERO.importer to process your
data using FileStitcher. However, I am not certain whether
OMERO.importer is currently capable of utilizing FileStitcher or not
-- perhaps Brian or Melissa can comment on that.

> I would like to have at least the channel info properly imported 
> within OMERO.

Bringing in channel metadata (e.g., wavelength, fluorescent label used,
etc.) directly from the filename is more challenging, and would take
some additional effort to handle. What we are working to support is
actually a more general purpose graphical metadata annotation tool that
would let you specify such details before, during or after import.

> I've tried creating a stack in imageJ, but it treats the channel 
> images as time points after import.  I've also tried the 5dImage 
> plugin to successfully create a 5D image that represents the images as

> channels (1 time point, 2 channels), but this fails during import in
OMERO.

I am not sure what you mean by "this fails during import in OMERO" -- as
far as I know there is no way to get data from within ImageJ into OMERO
directly, although we are planning to create an "Upload to OMERO" plugin
for ImageJ when we have time. Are you doing a "save as"
into a single file and then trying to import that merged file into
OMERO? Unfortunately, there is no multidimensional standard format to
which you can currently "save as" that is supported by OMERO.importer.
We are hard at work on support for OME-TIFF though, so soon you should
be able to export from ImageJ to OME-TIFF and then import that into
OMERO.

> After this I would like to manage tiles/sections (X/Y areas) taken 
> within one well (they are physically next to each other in the well so

> I understand these are part of one 5D image?)

The OMERO.insight client has some features relating to regions of
interest for individual image planes. If you elaborate more on exactly
what you want when you say "manage tiles/sections" we can comment
further on whether what you want is something that is supported or
planned.

-Curtis

On Nov 26, 2007 4:35 PM,  <Matthew.Smicker at sanofi-aventis.com> wrote:
> We are able to export files from a proprietary format into a 
> relatively metadata-free tiff format (unfortunately).  Multiple 
> channels are exported as separate files.  Filenames contain the 
> metadata (channel, well).
>
> I would like to have at least the channel info properly imported 
> within OMERO.
>
> Is there a way to either:
> 1 - manually assign this info after the fact (merge the 2+ images to 
> one and assign channels)
> 2 - merge the images in imagej for import info OMERO
>
> I've tried creating a stack in imageJ, but it treats the channel 
> images as time points after import.  I've also tried the 5dImage 
> plugin to successfully create a 5D image that represents the images as

> channels (1 time point, 2 channels), but this fails during import in
OMERO.
>
> After this I would like to manage tiles/sections (X/Y areas) taken 
> within one well (they are physically next to each other in the well so

> I understand these are part of one 5D image?)
>
>
> At this point I am not looking for a automated method.
>
> Thanks,
>
> Matt
>
> Matt Smicker
> Research Investigator, Screening & Assay Sciences Lead Identification 
> Technologies - BioS Department
>
> sanofi-aventis
> Bridgewater, NJ 08807-0800
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