[ome-users] ImarisHDF Reader: Do not show the series dialog

Wed Aug 23 16:16:08 BST 2017

Hi Eliana,

On 22 Aug 2017, at 13:26, Eliana Andreica <eliana.andreica at gmail.com<mailto:eliana.andreica at gmail.com>> wrote:

Hello David,

Thank you for your answer.

following up on behalf of David who is on leave for a few days.

I will take a look at the new options tab PR, maybe take it for a spin in my local copy.

About the use of flattened resolutions, we still have some questions. The first being about the utility of multiple resolutions in Bio-Formats. Does OMERO use the pyramid (with its original resolutions) in image rendering? (As far as we know, Fiji doesn't; please correct us if we are wrong.) In other words, why would you prefer option 2 over option 1 (from my previous email)?

The Bio-Formats sub resolution API [1] is definitely used by several consumers OMERO [2]
amongst other for accessing and rendering multi-resolution pyramidal images. Modifying the
coreMetadata on any reader would be a breaking change from a data layout perspective.

It is true that the Bio-Formats ImageJ plugin currently does not expose this particular API. Most
of the work on pyramidal images has been primarily driven by OMERO. But this limitation
has been raised to our attention lately [3].

From our perspective, enabling some configuration allowing to use the existing API i.e.

reader.setFlattenedResolutions(false);
reader.setResolution(0);

has the advantage of addressing your RFE while remaining fully compatible with all other usages.

Best,
Sebastien

[1] https://docs.openmicroscopy.org/bio-formats/5.6.0/developers/wsi.html
[2] https://downloads.openmicroscopy.org/omero/5.3.3/api/ome/io/bioformats/BfPixelBuffer.html
[3] https://trello.com/c/xWnT2XZC/67-imagej-plugin-flattened-resolutions

I will be back with feedback (and probably more questions) after I know more about the new tab.

Thank you,
Eliana Andreica

That’s great. We’ll make sure we notify you once the ongoing work is merged if you want to build
on top of it.

Best,
Sebastien

On Mon, Aug 21, 2017 at 4:40 PM, David Gault (Staff) <d.gault at dundee.ac.uk<mailto:d.gault at dundee.ac.uk>> wrote:
Hi Eliana,

Firstly, thank you for raising this feature request for discussion as it is always great to have the community getting involved in these decisions.

The storing of multi-resolution pyramids as a series when opened with ImageJ/Fiji is not always ideal. As you mentioned it is also not limited to Imaris but also affects many other formats. As such we would ideally prefer a solution that would be used across formats rather than on an individual level.

From some initial testing it would seem that the second solution using 'setFlattenedResolutions(false)’ could be a straight forward solution that could be implemented in the Bio-Formats plugin and used across formats. Ideally this should also be configurable as you put forward in the third solution. We have recently been working on an unrelated PR (https://github.com/openmicroscopy/bioformats/pull/2891) which will add a new options tab to the Bio-Formats plugin configuration window for the purpose of cross reader import options. Perhaps this new Bio-Formats options tab would be a good place to add a configuration option for flattened resolutions. I have attached a screenshot with a mocked up an example of how this new options tab could be used.

<Screen Shot 2017-08-21 at 15.34.46.png>

With Thanks,
David Gault

On 18 Aug 2017, at 15:33, ANDREICA Eliana <e.andreica at bitplane.com<mailto:e.andreica at bitplane.com>> wrote:

Hello,

I should start by saying that this is a feature request (that we will implement if approved), not a bug report.

The current behavior of the ImarisHDF reader is to show a series dialog for the multi-resolution pyramid(s) contained in an IMS file. The pyramid is not a series in the usual series sense as it just contains different resolutions of the same image. We believe that generally, users are interested in the full resolution image. Therefore we (at Bitplane) propose to open the full resolution image without showing the series dialog.

We considered three alternative ways to get rid of the series dialog and propose these here:

1) We keep in core metadata only the highest resolution of the (first) pyramid.

2) We use setFlattenedResolutions(false) and populate core metadata with a pyramid of as many low resolution versions of the highest resolution image as is possible from the IMS file (sometimes not possible to use all resolutions from IMS since the IMS pyramid may downsample Z). These actions will make getSeriesCount() return 1, so that the series dialog will not show. It is not entirely clear to us whether it is of value for any part of Fiji to store the lower resolutions of the pyramid.

3) We don't modify the number of series. We make the series dialog optional (with the default = off), by adding a new checkbox, "Show lower resolutions", under Memory Management. I implemented that in my local copy, just to see what it would involve. Of course, a new checkbox for only one format (and conditioned so that its state is read only in case of that format) is not particularly desirable. We are just mentioning this alternative here, because maybe there are some other formats that would benefit from it? We don't know.

Please let us know if you think Bio-Formats could accommodate our feature-request and which of the three alternatives you would prefer. We will then open a pull request for that option.

We are aware of the windowless option in Bio-Formats, but with this request we intend to improve the workflow for users who use File->Open. We are also aware of the possibility of enabling ImageJ2 but we would like to deliver this to the majority of users asap.

Thank you,

Eliana Andreica

The University of Dundee is a registered Scottish Charity, No: SC015096

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