Metamorph_nD_5D

FIJI plugin for fast virtual hyperstack loading of Metamorph format "Multi-Dimensional acquisition" nd files (TIF series).
Works with multi-wavelength/time/z-slices/positions 5D images.

To install, copy Metamorph_nD_5D-X.X.X.jar file from the latest release to your FIJI plugins folder.

NB: Currently the plugin assumes that all tiffs are 16-bit.

Usage

At the initial file chooser dialog, select Metamorph's file ending with nd.
The following dialog should appear:

• First option is the position to be loaded.
• "Max cache/memory size" parameter specifies, how much maximim memory (RAM) the virtual hyperstack will occupy. It is measured in the size of individual XY frames. So this number of "last visited" frames will be kept in memory, the rest will be readed "on-the-fly" from the disk.
• In case of "Adjust image dimenstions?" hyperstack voxel size/time interval and units will be set with provided values.
• "Do not open image, just show info in Results" will do just that, show Results Table with dataset parameters.

The plugin is scriptable using ImageJ macro (use Recorder to see parameters), for example:
run("Metamorph 5D reader X.X.X", "open=/home/eugene/testing.nd load=[Position 1] max=10");

Motivation

The reason for this plugin is that a "standard" BioFormats reader, before loading files to Virtual stack, checks all underlying tiff files for consistensy. This process can take a while in case of large datasets containing multi-position/channel/z-slices. This plugins assumes all tiff's configurations are the same. It reads the first TIFF and loads the rest of them with its settings. You can read a bit more about it here.

The plugin is based on examples shown at these one, two discussion topics at image.sc forum.

Updates history

0.0.4

Fixed error for TIF/STK shift for different wavelengths. It caused horizontal image shift in some wavelength/z-stacks.

0.0.3

Fixed opening error if files are stored as .STK

0.0.2

Added an option to show info only in Results, without loading images.

0.0.1

First release

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Developed in Cell Biology group of Utrecht University.
E-mail me for any questions.