Added support for multiple samples in raw/ (#540) #516

Job	Run time
setup	55s
ex002	33m 0s
ex001-by-step	16m 28s
ex001 (--viz)	11m 18s
ex001 (--start-at illumination --stop-at registration)	2m 35s
ex001 (--background)	11m 30s
ex001 (--background --background-method imagej-rolling-ball)	12m 39s
ex001 (--segmentation cypository --cypository-opts '--channel 10 --scalingFactor 2' --s3seg-opts ...	10m 20s
ex001 (--segmentation ilastik,mesmer)	4m 51s
ex001 (--segmentation cellpose --mcquant-opts '--masks *masks.tif')	7m 40s
ex001 (--viz --segmentation ilastik -profile singularity)	14m 39s
	2h 5m 55s

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