Allows loading of image data in NDTiff format into MATLAB. The NDTiff file format is utilized by Micro-Manager and Pycro-Manager and is a more efficient alterantive to the conventional TIFF and OME-TIFF formats. This package loads multi-dimensional datasets into intuitively-shaped 4-D or 5-D matrices, supports accessing only desired regions of the data, and provides access to the summary metadata.

• Clone this repository or download the .m files and place them in your MATLAB working directory (or add them to your MATLAB path).
• Download and install a recent Micro-Manager Nightly Build.
• In the Micro-Manager installation directory, locate these two files: ../plugins/Micro-Manager/MMCoreJ.jar and ../plugins/Micro-Manager/NDTiffStorage-#.#.#.jar (replace #.#.# with the actual version number included in your nightly build).
• In your MATLAB installation directory, find the Java Classpath file, which is located at $MATLAB\toolbox\local\classpath.txt. Open it. Add two lines to the end of this text file, one containing the complete path to each of the .jar files above. For example, on my machine, these two lines are:
  /Applications/Micro-Manager-2.0.3-20250818/plugins/Micro-Manager/MMCoreJ.jar and
  /Applications/Micro-Manager-2.0.3-20250818/plugins/Micro-Manager/NDTiffStorage-2.18.4.jar.
  Save and close the classpath file. Launch (or re-launch) MATLAB and you are ready to go.

To load an entire NDTiff dataset into memory, use the command
[image, smd] = loadNDTiffDataset(<path/to/dataset>);
where the path should point to the directory containing your NDTiff file(s) and the NDTiff.index file. Provide the path to the directory, not the .tif file.
image will be a multi-dimensional array containing the image data, in the dimension order x, y, c, z, t, pos. Any singleton dimensions are skipped.
smd will be a MATLAB structure containing the summary metadata.

You can also load a subset of the data by specifying the optional subregion, channels, frames, slices and positions arguments.
For example, to load only channel 2 of a 3-color dataset, use the command
[image, smd] = loadNDTiffDataset(<path/to/dataset>, 'channels', 2);
To load only z planes 2-4 of a dataset containing more z planes, use
[image, smd] = loadNDTiffDataset(<path/to/dataset>, 'slices', 2:4);

To determine the size of a dataset (how many channels, slices, frames etc. it contains), use
[x, y, c, z, t, p] = getNDTiffImageSize(<path/to/dataset>);

Currently this package only supports reading NDTiff files. Any modified data will need to be saved in conventional TIFF or another format, for example using MATLAb's built-in imwrite function. Support for writing NDTiff files may be added in a future version.