Mastodon: Diverse Questions

Yes.

That is the ImgLoader, yes. To not require the above “special” opening command, we need to make an
XmlIoImarisImageLoader class that can be de/serialized into XML and then automatically be discovered. Basically the XML would look like this:

<?xml version="1.0" encoding="UTF-8"?>
<SpimData version="0.2">
  <BasePath type="relative">.</BasePath>
  <SequenceDescription>
    <ImageLoader format="imaris">
      <ims type="relative">somefile.ims</ims>
      <additional parameters .../>
      <additional parameters .../>
      <additional parameters .../>
    </ImageLoader>
    ...

The task of XmlIoImarisImageLoader is to read/write the <ImageLoader format="imaris"> portion.
It can be relatively simple (see XmlIoRemoteImageLoader mentioned above), but will need some additional parameters (see ImarisImageLoader constructor).

Once XmlIoImarisImageLoader exists, for an existing ims file, it would be as simple as

final SpimDataMinimal spimData = Imaris.openIms( file.getAbsolutePath() );
new XmlIoSpimDataMinimal().save( spimData, "./imaris.xml" );

to create an XML file that can be used in Mastodon, BigDataViewer, Labkit, etc.

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ok!

frankly speaking I will probably have only time to go for the quick fix (a) this week.

[EDIT]: I implemented solution (a), but then I ran into another issue when trying to export the results, because the code also here expected an .xml: https://github.com/fiji/TrackMate3/blob/9aa9a6fb44c2ed88a917710ae34b436a198ff9ae/src/main/java/org/mastodon/revised/model/mamut/trackmate/MamutExporter.java#L453
so maybe, I should indeed work on making an XmlIoImarisImageLoader

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I have also some simple usage question: If I want to move a spot along the current z-plane: How do I do it? Do I need to rotate the BDV view? Or is there some other way?

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No other way.
The transform is fixed while you move the spot and you cannot change z plane.

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Btw any chance we could close this topic once it received a satisfying answer :wink: ?

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Well, the topic is “Mastodon: Diverse Questions” :slight_smile:
You think it would be better if I opened a new post for each question? I guess you are implying it would. I’ll do so.

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Related to that: we also need to implement a Bdv reader for the OME pyramidal Tiff format. We also need to be able to associate and AffineTransformation with each Tiff, because we need to show several of them together in a common coordinate system. I guess one route to achieve this would be to implement a XmlIoPyramidalTiffImageLoader?

cc @joshmoore

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Hi Christian,

I think another topic would help indeed :wink: . For this specific topic, you should have a look at this repo we are working on: https://github.com/BIOP/bigdataviewer-bioformats

It’s a bioformat reader aimed for BigDataViewer. It uses the general way bioformats handles pyramidal formats, and fits it into BigDatViewer logic. Thus it works not only for pyramidal ome tiff, but also for vsi datasets for instance (multi series multi pixel type + pyramidal). With this repo that you can create your dataset for BigDataViewer, including pyramidal ome-tiffs.

Best,
Nico

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Wow! I am speechless! Looks very good!

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