bgorissen

You should call runHarmony with eigs.dim instead of eigs.dims. The [example](https://github.com/r3fang/SnapATAC/tree/master/examples/10X_snATAC) provides the following code: ``` > library(harmony); > x.after.sp = runHarmony( obj=x.sp, eigs.dims=1:22, meta_data=x.sp@sample # sample index ); ```...

This error occurs due to spaces in the folder or file name. The arguments to snaptools should be between quotes (but currently they are not).

You may get this error if you don't pass a conservation_file.

Could you still add support for 16 bit single channel files? Such images are commonly used in fluorescent microscopy, and storing them in jxl instead of tiff or png would...

> Any relation-to or overlap-with #1888 here? 🤔 Not quite, fluorescent microscopy images are often stored in a single channel while #1888 is about multichannel files. Pillow already supports single...

@[olokelo](https://github.com/olokelo) I've attached a 16-bits grayscale jxl file (zipped because Github does not support jxl). You could crop it to create a smaller test file. The file was converted from...