ROADMAP

In general nd2tool tries to keep the number of dependencies at a minimum and will not try to compete in features with other existing tools.

To do

Collect various nd2 files for testing, at the moment not tested on time series at all (feel free to share your data).
Indicate where the most in focus slice is.
Support MACOS
Warn/indicate of images are overlapping.
Store a XXH3 or MD5 hash of the nd2 file in the log.

Enable shake detection by default.
check that the channel names are valid file names?
As alternative to the Nikon library, consider adopting from Open-Science-Tools/nd2reader.
Write tiff files without the tiff library like on fTIFFw for some extra speed.
bash auto-completion.
Option to export one file per FOV, channel and z-pos.
Custom color maps for multi channel images.
Include support for czi images. Zeiss now has a public library at [https://github.com/ZEISS/libczi] however it is C++ only so we would have to add a wrapper.

Option to export as multi-color tif files. -- Requested in issue #1 This was implemented in version 0.1.3 and is enabled with the --composite flag.
Check for inconsistent dz values between image planes (shake detection with --shake).
Export position of images as csv file (--coord).
Supports writing BigTIFF images, i.e., > 2 Gb (at least one image of size 14607 x 14645 x 17 worked out fine).
Include Nikon's nd2-library in the repo.
Metadata about resolution is transferred from nd2 files to tif files so that the correct resolution is found by ImageJ.
It is checked that the image data is stored as 16-bit, otherwise the program quits.
One log file is written per nd2 image that is converted.
Only keeps one image plane in RAM at the same time in order to keep the memory usage low.
Safe writing: Using a temporary file (using mkstemp) for writing. Renaming the temporary file to the final name only after the writing is done. Prevents corrupt file being written. Will leave files like file.tif_tmp_XXXXXX upon failure that has to be removed manually.