Added support for multiple samples in raw/ #515

Job	Run time
setup	1m 0s
ex002	32m 36s
ex001-by-step	16m 33s
ex001 (--viz)	11m 30s
ex001 (--start-at illumination --stop-at registration)	2m 20s
ex001 (--background)	11m 6s
ex001 (--background --background-method imagej-rolling-ball)	12m 21s
ex001 (--segmentation cypository --cypository-opts '--channel 10 --scalingFactor 2' --s3seg-opts ...	10m 39s
ex001 (--segmentation ilastik,mesmer)	5m 9s
ex001 (--segmentation cellpose --mcquant-opts '--masks *masks.tif')	7m 7s
ex001 (--viz --segmentation ilastik -profile singularity)	14m 1s
	2h 4m 22s

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