Non rectangular images - Coordinates - Multiple channel extraction

[MathieuBo]

Hi all,

Thanks a lot for developping such a great tool. I have three questions:

• Can the package handle non rectangular pictures?
• What is the benefit of using stage coordinates vs tile order (1_1, 1_2, 2_1, 2_2 for example)? Will the stitching be more accurate with stage coordinates? I tried with just a rough tile ordering and it worked extremely well already.
• A channel argument can be passed to extract R,G,B channels selectively. What would be the best strategy to stitch a multichannel picture? If the yml file is generated based on a reference channel (e.g. DAPI), can stitch-fusebe run on another one?

Thanks a lot for your help! Mathieu