About

Here's the home of the Fiji wrapping plugins that bring OME.Zarr (at specs 0.4) to Fiji, currently only for the reading.

Several ways of importing a zarr container are supported:

Using Fiji menus

Try: Fiji -> File -> Import -> OME.Zarr... -> Open Zarr* menu items

By dragging and dropping...

...the top-level zarr folder onto the Fiji main window (video, 49 secs). Both options can lead to opening of a dialog

that

• offers options of showing the zarr content,
• controls the effect of the drag-and-drop event.

One can use this dialog to (repetitively) adjust the behavior of the drag-and-drop -- just don't forget to press 'OK' button in that dialog (it's not enough to adjust the toggles and close it, it won't be remembered).

Programmatically...

...from the ImageJ macros,

and from Jython scripts.

Example code can be downloaded from the examples folder.

Installation

Three pieces of software are (at least) needed:

• modified ij-1.xxy.jar according to the fix by Ko Sugawara
• extended mobie-io-1.2.13.jar from Christian Tischer's github
• the ome-zarr-fiji-ui-0.1.0.jar from this repository (master branch).

You can also get them from the jars folder and drop them into your Fiji installation, into its jars folder from which it's original ij-1.xxy.jar should be removed first.

Authors

This is a result of collective work of several people noted below, during the Fiji and Zarr hackathon 2022 in Prague, CZE, which was generously supported by the IT4Innovations National Supercomputing Centre, Ostrava, CZE:

• forum.sc link,
• zulip link,
• link at IT4I.

The people on-site during the hackathon:
Ko Sugawara, Nils Norlin, Tobias Pietzsch, Christian Tischer, Vladimir Ulman

The people online during the hackathon:
Gabor Kovacs, Isaac Virshup, Luca Marconato, John Bogovic, Josh Moore

I want to thank all of them for devoting their time so far to this project.