[ome-devel] Is OME-TIF file with 2 image series of different pixel types supported?

Fri Dec 2 16:45:48 GMT 2016

Hi Michael,

> Since I will need the ability to stream frames, and all my frames will
> be of same size and type, I’ll write the frame data to disk as it is
> collected and the populate the OME.TIFF file by recovering the frames
> from disk. Not ideal but not too much work.

For what it's worth, here is how we do it at LOCI with our WiscScan laser
scanning software:

During the run:

- Acquire TIFF frames, writing them to individual files on disk.

- Keep an OME-XML data structure in memory which is continuously updated as
the acquisition proceeds.

- Write a snapshot of the OME-XML block to a temporary file on disk, in
case the run crashes.

At the completion of the run:

- Rewrite all TIFF frames into the final desired organization—in our case,
one TIFF file per time point and channel, with all Z positions in the same
file.

- Generate the final OME-XML block from the OME-XML data structure,
injecting it into every 10th TIFF file.
 -- The other 9 TIFFs receive a "partial OME-XML metadata" stub as
described in the OME-TIFF specification [1].
 -- This provides some redundancy of metadata without bloating the size of
all TIFF files.

It is also feasible not to rewrite the TIFFs ever, and instead efficiently
inject the final OME-XML into each existing TIFF file. The Bio-Formats
library provides convenience methods for doing this [2], as long as you
write a stub ImageDescription initially.

In this way, it is possible to do e.g. streaming acquisition, and
ultimately end up with OME-TIFF.

Regards,
Curtis

[1]
http://www.openmicroscopy.org/site/support/ome-model/ome-tiff/specification.html#partial-ome-xml-metadata
[2]
https://github.com/openmicroscopy/bioformats/blob/v5.2.4/components/formats-bsd/src/loci/formats/tiff/TiffSaver.java#L892-L897

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/

On Fri, Dec 2, 2016 at 10:06 AM, Michael Ellis <michael.ellis at dsuk.biz>
wrote:

>
> On 2 Dec 2016, at 15:40, Roger Leigh <rleigh at dundee.ac.uk> wrote:
>
> On 01/12/16 15:26, Michael Ellis wrote:
>
> Dear Roger
>
> The main body of my code can be seen
> here: https://cloud.karyotyper.com/s/K9SoEKgLOcbgwTg
>
> CaptureImages is essential a sorted ArrayList of CaptureImage
> CapturedImage is a BufferImage that has a Map<String, Object> associated
> with it for additional image properties such as channel name, colour,
> stage position, exposure time etc.
>
> My BioFormatsWriter class interrogates those extra image properties to
> build the extra metadata.
>
> Because BioFormats has to have all metadata constructed before writing
> the pixel data, this  BioFormatsWriter simple implementation
> construct all the metadata as each image series is added with the
> addSeries() method, and then actually writes the images data when it
> gets to the close() method.
>
>
> I checked through the OMETiffWriter code, and unfortunately it does
> require all the image series' to be present up-front.
>
> https://github.com/openmicroscopy/bioformats/blob/develop/components/
> formats-bsd/src/loci/formats/out/OMETiffWriter.java#L218
>
> This could potentially be made more general, but will require more
> thought about its implications.  The writer is currently oblivious to
> the subsequently added image series', which is why it's unfortunately
> not working properly as it stands.
>
>
> Since I will need the ability to stream frames, and all my frames will be
> of same size and type, I’ll write the frame data to disk as it is collected
> and the populate the OME.TIFF file by recovering the frames from disk. Not
> ideal but not too much work.
>
>
>
>
> Some pointers in regards to what “is not facet-valid with respect to
> pattern '(urn:lsid:([\w\-\.]+\.[\w\-\.]+)+:\S+:\S+)|(\S+:\S+)’” would be
> much appreciated too.
>
>
> Here the above regular expression is used to validate the "ID"
> attributes for various elements.  The default is to match the (\S+:\S+)
> pattern by using identifiers like "Instrument:0", "Channel:1",
> "FilterSet:2" and so on.  I think use of "Fitc" and "TxRed" as Filter
> IDs is not matching; you could use e.g. "Model" here as a description,
> though the most user-visible place is probably on Channel "Name" if you
> want it visible in user interfaces.  The same applies to
> "EmulatedCamera_0" on Detector; this is expecting Detector:n as the ID;
> "Model" is likely the most appropriate attribute here for the camera
> name.  A shorthand Name attribute would perhaps be a convenient addition
> to the model for these components, as a shorthand reference, since the
> ID is essentially a primary key with a strict naming requirement.
>
> Yes, that is a terrific help and I will look to make my code comply.
>
>
>
> I hope that helps, please let me know if there's anything you'd like
> explaining further.
>
>
> I am very appreciative of the help you have offered. I am writing a
> computer assisted microscope application and storage of multiple 5D images
> with associated metadata has to be tackled one way or another. Rolling my
> own was not an attractive option especially since ImageJ will be one
> popular end points and if the ImageJ BioFormats Importer plugin does a half
> decent job, then I have a real benefit for zero (extra) effort.
>
> Again many thanks!
>
>
>
>
>
> Regards,
> Roger
>
> --
> Dr Roger Leigh -- Open Microscopy Environment
> Wellcome Trust Centre for Gene Regulation and Expression,
> College of Life Sciences, University of Dundee, Dow Street,
> Dundee DD1 5EH Scotland UK   Tel: (01382) 386364
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
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>
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