Convert NDTiff with non-HCS position labels

[ziw-liu]

          > We should test that these new datasets are correctly converted to zarr, whether they carry HCS or 'Pos0'... position labels

I am guessing that this segment will need to be modified to provide string indices for the position and channel axes, rather than integers. These should be obtained from NDTiffReader._axes, such that you call dataset.as_array(position='Pos1',...) rather than dataset.as_array(position=1,...)

iohub/iohub/convert.py

Lines 254 to 263 in 1ae2737

	# create array of coordinate tuples with innermost dimension
	# being the first dim acquired
	self.coords = [
	(dim3, dim2, dim1, dim0)
	for dim3 in range(dims[3])
	for dim2 in range(dims[2])
	for dim1 in range(dims[1])
	for dim0 in range(dims[0])
	]

Do you mean that the converted OME-Zarr will have path names that reflect non-HCS MM stage position labels? Currently we put each position in a separate well in a single row, will this behavior be preserved, thus producing FOV paths 0/Pos000/0, 0/Pos001/0 etc?

Originally posted by @ziw-liu in #166 (comment)