Loaded OME-Zarr opens at a specific user-given resolution

[xulman]

A user request has been encountered during the Image Data Community Days 2026:

Is it in your development timeline to also offer to load at a specific resolution? 
I have users who would benefit from something like this for multimodal imaging
if both datasets could be open at the same resolution.

And, indeed, it is true that the current setting of the DnD is that either

• always the 1st (highest res) level is "opened",
• or it auto-chooses (based on the max preferred with DnD option).
• (One cannot request to always have the 3rd res level opened, for example.)

But since multimodal imaging and both datasets are mentioned. The desired functionality is probably

• User presets desired width, e.g., 654 pixels, and the DnD chooses the closest wider pyramid and downscales to 654 before opening it in Fiji.

Shall we support this, and how?

[xulman]

This is basically about having two (or more) datasets displayed in the same window (each dataset as, e.g., one layer -- the usual setup) and having them transformed such that the content aligns. In the user story above the transformation is probably only scaling (so that all displayed images end up displayed at the same pixel width, and height, and depth.....

I'm seeing the following options:

Variant 1 - Wait for the upcoming OME-Zarr standard

This fits the goal of the NGFF RFC5 just perfectly. And this today really is on the horizon, see the pre-final v0.6 specification, the Scene part.

Variant 2 - Run a script that opens two OME-Zarrs in one BDV

In the meantime, or if explicit transformation information is not available, one could have the two datasets displayed in one BDV, and use the manual transformation feature of the BDV (tutorial video here, don't mind it is for BigStitcher, it works the same for BDV).

Just copy and paste the following Jython snippet into Fiji's Macro editor (and make sure Python (Jython) interpreter is selected in the Languages menu of the editor).

#@ BdvHandleService bdv
#@ String pathA (label = "Path to the first OME-Zarr")
#@ String pathB (label = "Path to the second OME-Zarr")
#@ Context ctx

from sc.fiji.ome.zarr.pyramid import DefaultPyramidal5DImageData

zarrA = DefaultPyramidal5DImageData(ctx, pathA)
bdv.openNewBdv(zarrA.asDataset().getImgPlus(), zarrA.getName())

zarrB = DefaultPyramidal5DImageData(ctx, pathB)
bdv.addToLastOrInNewBdv(zarrB.asDataset().getImgPlus(), zarrB.getName())

This opens one BigDataViewer window in which two datasets are opened simultaneously. Most likely, one may need to adjust the brightness and contrast (and color tone of each dataset to distinguish visually among them) using the right-hand-side pop-up panel of BDV (press P to open it).

Variant 3 - Use an open-and-resize script with the DnD dialog

Utilize the User script feature of the DnD dialog, and set it up (Fiji -> Plugins -> OME-Zarr -> Drag & Drop User Script Settings) to use the script below. That said, copy and paste the following Jython snippet into Fiji's Macro editor and save it, e.g., as /some/path/open_and_resize.py. The suffix must be .py. This would be the path to provide to the User Script Settings dialog.

#@ String path
#@ Context ctx
desired_width = 768

from sc.fiji.ome.zarr.pyramid import DefaultPyramidal5DImageData
from net.imglib2.img.display.imagej import ImageJFunctions

# strips away the URL prefix: 'file://' 
path = path[7:]
max_width = int(desired_width*1.99)
print("going to open path: "+path)
print("choosing res no wider than (px): "+str(max_width))
zarr = DefaultPyramidal5DImageData(ctx, path, max_width)

imp = ImageJFunctions.wrap(zarr.asDataset().getImgPlus(), zarr.getName())

w = imp.getWidth()
h = imp.getHeight()
new_h = int( (float(desired_width) / float(w)) * h )
print("resizing from "+str(w)+"x"+str(h)+" to "+str(desired_width)+"x"+str(new_h))

imp = imp.resize(desired_width, new_h, 1, "bilinear");
imp.show()

The target size is hard-coded in the script in the line desired_width=, in pixels.

This script gets a path from the DnD mechanism, it opens an OME-Zarr at that path and loads from it the resolution pyramid level that's not wider than nearly twice the desired_width (basically, it asks for the nearest larger resolution level... I hope). Then it rescales and shows in Fiji. This rescaling is a problematic part as it duplicates memory!

TODO for Vlado: Utilize Imglib2's View mechanism to scale on the fly and only that provide/expose to Fiji.