[ome-devel] Trello Bio-Formats 5.6.0 board closed / ImageJ BioFormats Image Importer Plugin

Fri Aug 18 08:02:06 BST 2017

Dear Sebastien,

I had not realised that there was a FileInfo hook from which I could get the entirety of the BioFormats metadata. I will investigate using this and expect to answer all my needs!

Many thanks for this most helpful reply.

— ME
> On 17 Aug 2017, at 22:29, Sebastien Besson (Staff) <s.besson at dundee.ac.uk> wrote:
> 
> Hi Michael
>> On 16 Aug 2017, at 11:05, Michael Ellis <michael.ellis at dsuk.biz <mailto:michael.ellis at dsuk.biz>> wrote:
>> 
>> Dear all,
>> 
>> ITAC?= Is This Assumption Correct?
>> IJBFIIP = ImageJ BioFormats Image Importer Plugin
>> 
>> I am at a loss, can you point me in the right direction?
>> 
>> Sometime back I submitted a pull request on the IJBFIIP so that image slice labels could be set from channel names stored within .OME.TIFF files.
>> 
>> I was informed this pull request would be shelved as it amounted to a functional change and not just a bug fix.
>> 
>> Eventually I was pointed at using Trello and to follow the  Bio-Formats 5.6.0 board. This I did and added some further comments in relation to the proposed final solution.
> 
> For full reference, the design discussion took place in [1] and the proposed implementation is available in [2].
> 
>> I sit, i wait, I soldier on with my own patch to the IJBFIIP.
>> 
>> Yesterday I see that the Trello Bio-Formats 5.6.0 board is closed and I do not know where to go to track what is happening to the proposed changes for the next major release?
> 
> We had certainly planned to include this feature as part of 5.6.0. Unfortunately, the last
> round of reviews were not meeting all quality criteria. Thus we decided to postpone the
> delivery of this feature to an upcoming patch release of Bio-Formats 5.6.x.
> 
> At this stage, subscribing to the open Pull Request is certainly the best option to track
> changes. Once merged, they will be included in the following release of Bio-Formats.
> 
>> Further, I am implementing a computer assisted microscope package (SmartCapture 4), I’ve chosen to use the BioFormats.jar package and save in OME.TIF format as this is a nigh on perfect match for our requirements of being able to save 5D images will instrument and experiment metadata - Yipee!
>> 
>> My intention is for SmartCapture 4 to hand off image processing to other applications, principally  ImageJ/Fiji and our own SmartType karyotyping application. Transferring images as OME.TIF files is ideally suited.
>> 
>> However, I do have further observations in respect of the IJBFIIP that I would at least like to put forward without feeling they these requests just disappear into the wind.
>> 
>> Specifically,
>> 
>> If the .OME.TIF file format is considered the most complete or canonical image file format for OME metadata (ITAC?) then it would seem at least desirable that the IJBFIIP utilise as much metadata from  .OME.TIF files as possible (for instance channel colour as well as channel name).
>> 
>> I do see that there is a potential for semantic mismatches or ambiguities in how some metadata might be used, but even if only a part of the metadata is used to set ImageJ ImagePlus image properties, should not *all* the metadata be accessible *after* the IJBFIIP has completed the import?
>> 
>> The argument that I can patch IJBFIIP and do whatever I want seems a weak one. If I have to patch the IJBFIIP, I am burdened with having to track and merge all of your changes (as will anyone else wanting something extra from the metadata).
>> 
>> My suggestion (is this already possible?), is that the IJBFIIP provides a mechanism for accessing the metadata for any ImageJ ImagePlus that has been imported by the IJBFIIP.
>> 
>> If (as I suspect) there is no hook on an ImagePlus for hanging the XML metadata, then perhaps this could be hived off into a file and reference to that file could be attached to the ImagePlus? I’d then at least be able to write my own ImageJ plugins that could inspect an ImagePlus, determine if it had associated OME data and use the BioFormats.jar library to gain access to the extra metadata without having to have my own version of the IJBFIIP.
> 
> With regard to the hook for the metadata, the Bio-Formats ImageJ plugins populate
> the FileInfo of the created ImagePlus objects with various information including
> the metadata in the description attribute.
> 
> With the current version of the plugin, you should be able to inspect the metadata
> using the ImagePlus.getOriginalFileInfo() API [3]. In the OME-TIFF case, the description
> attribute should include the metadata that is also stored in the ImageDescription tag of
> the file.
> 
>> I really want to make use of BioFormats, it’s such a perfect match for our needs. But, having IJBFIIP filter our so much of the metadata seems just counter intuitive if, as I suspect, ImageJ is the most widely used application for reading OME.TIF files?
> 
> Putting precise numbers on the usage of individual file formats is always challenging
> but it is correct that from our perspective, the ImageJ/Fiji ecosystem certainly remains
> one of the most important community where Bio-Formats is consumed.
> 
>> With best regards to all — Michael Ellis
>> Digital Scientific UK Ltd
> 
> Best,
> Sebastien
> 
> [1] https://trello.com/c/KHxM1IIe/1-imagej-imageplus-slicelabel-modification <https://trello.com/c/KHxM1IIe/1-imagej-imageplus-slicelabel-modification> 
> [2] https://github.com/openmicroscopy/bioformats/pull/2891 <https://github.com/openmicroscopy/bioformats/pull/2891>
> [3] https://imagej.nih.gov/ij/developer/api/ij/ImagePlus.html#getOriginalFileInfo-- <https://imagej.nih.gov/ij/developer/api/ij/ImagePlus.html#getOriginalFileInfo-->
> 
>> 
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