Fiji and ImageJ

Fiji reads CZI, ND2 and LIF files with its bundled Bio-Formats importer, so you do not need OpenReadout just to look at a file. OpenReadout is still useful alongside Fiji in three ways:

Before opening: openreadout check tells you whether a large file is complete, and openreadout info what it holds, without starting Java.
For sharing: an exported OME-TIFF opens in Fiji, QuPath, napari, Python and OMERO, with no vendor reader needed on the other side.
As a second opinion: OpenReadout and Bio-Formats were written independently. If they disagree about a file, one of them has a bug. Please open an issue.

Open an export

openreadout export run.czi -o run.ome.tiff

In Fiji, choose File › Import › Bio-Formats, pick run.ome.tiff, and choose Hyperstack view and Composite colour mode. The dimensions, channel names and pixel size (Image › Properties) come from the OME-XML that OpenReadout wrote. Dragging the file onto the Fiji window also works.

If you only need part of a large file, export only that part:

openreadout export big.nd2 -o pos3_gfp.ome.tiff --image 3 --select c=1 --select t=0-9

Use OME-TIFF for Fiji. Whether your Fiji opens OME-Zarr (--to ome-zarr, which writes OME-NGFF 0.5 on Zarr v3) depends on the version of its Zarr plugins.

From a macro

An ImageJ macro can run the program with exec and open the result with Bio-Formats. Save this as openreadout_open.ijm and run it from Plugins › Macros › Run…:

// Check a raw file, export it to OME-TIFF with OpenReadout, open the export in Fiji.
input = File.openDialog("Instrument file (CZI, ND2, LIF)");
output = File.getDirectory(input) + File.getNameWithoutExtension(input) + ".ome.tiff";

report = exec("openreadout", "check", input);
if (indexOf(report, "PROBLEMS FOUND") >= 0) {
    if (!getBoolean("openreadout check found problems:\n\n" + report + "\nExport anyway?")) exit();
}

result = exec("openreadout", "export", input, "-o", output, "--overwrite");
print(result);
if (indexOf(result, "verified=true") < 0) exit("Export failed:\n" + result);

run("Bio-Formats Importer", "open=[" + output + "] color_mode=Composite view=Hyperstack stack_order=XYCZT");

On macOS, an application started from the Dock does not get your shell’s PATH. If exec cannot find openreadout, use its full path, for example /Users/you/.local/bin/openreadout.

Many files

To convert a whole folder, run the export outside Fiji, then point Fiji’s batch tools (Process › Batch › Macro…) at the exported OME-TIFFs. openreadout export takes a directory and writes an OME-TIFF next to each file it recognizes:

openreadout export raw/ --recursive --skip-unknown --jsonl > export-log.jsonl