. 2020 Nov 29;11(1):315–329. doi: 10.1080/19491034.2020.1845012

Table 1.

OMERO-FSU Datasets

DATASET NAMES	ACQUISITION SYSTEM	DATASET NAMES	LINK	KEY FILTER	VALUE FILTER
#1 DIGITIZED SPHERES	Wide-field + OptoGrid	#1a DIGITIZED SPHERES – RAW	dataset-4902	RAW	DIGITIZED	6
		#1b DIGITIZED SPHERES – SEGMENTED	dataset-4901	SEGMENTATION	OTSU	6
		#1b DIGITIZED SPHERES – SEGMENTED	dataset-4901	SEGMENTATION	GIFT-WRAPPING	6
#2 FLUORESCENT MICROSPHERES	Wide-field + OptoGrid	#2a FLUORESCENT MICROSPHERES – ACQUISITION	dataset-4903	RAW	WIDE FIELD STACK	17
		#2b FLUORESCENT MICROSPHERES – AUTOCROP	dataset-4951	PICTURE TYPE	Z MAX PROJECTION	17
		#2 c FLUORESCENT MICROSPHERES – RAW	dataset-4952	RAW	DAPI CROP	81
		#2 c FLUORESCENT MICROSPHERES – RAW	dataset-4952	RAW	FITC CROP	97
		#2d FLUORESCENT MICROSPHERES – SEGMENTED	dataset-4953	SEGMENTATION	OTSU	157
		#2d FLUORESCENT MICROSPHERES – SEGMENTED	dataset-4953	SEGMENTATION	GIFT-WRAPPING	157
#3 NUCLEAR MORPHOLOGY	Wide-field + OptoGrid	#3a NUCLEAR MORPHOLOGY – ACQUISITION	dataset-4954	RAW	WIDE FIELD STACK	63
		#3b NUCLEAR MORPHOLOGY – AUTOCROP	dataset-4955	PICTURE TYPE	DIC	63
					Z MAX PROJECTION	63
					OVERLAY	63
		#3 c NUCLEAR MORPHOLOGY – RAW	dataset-4956	RAW	DAPI CROP	1554
		#3d NUCLEAR MORPHOLOGY – SEGMENTED	dataset-4957	SEGMENTATION	OTSU	1554
		#3d NUCLEAR MORPHOLOGY – SEGMENTED	dataset-4957	SEGMENTATION	GIFT-WRAPPING	1553
		#3e NUCLEAR MORPHOLOGY – RAW BAD CROPS	dataset-5009	RAW	BAD CROP	102
#4 CHROMATIN ORGANIZATION	Wide-field + OptoGrid	#4 CHROMATIN ORGANIZATION – RAW	dataset-5018	SEGMENTATION	THRESHOLD WATERSHED	315
#5 180BP_5S DNA FISH	Wide-field + OptoGrid	#5a 180BP_5S DNA FISH – ACQUISITION	dataset-5010	RAW	WIDE FIELD HYPERSTACK	8
		#5b 180BP_5S DNA FISH – AUTOCROP	dataset-5011	PICTURE TYPE	DIC	4
					Z MAX PROJECTION	4
					OVERLAY	4
		#5 c 180BP_5S DNA FISH – RAW	dataset-5012	RAW	CY3 CROP	160
					CY5 CROP	149
					DAPI CROP	160
		#5d 180BP_5S DNA FISH – GIFT SEGMENTED	dataset-5015	SEGMENTATION	GIFT-WRAPPING	159
		#5e 180BP_5S DNA FISH – FISH SIGNALS	dataset-5016	SEGMENTATION	CY3 THRESHOLD WATERSHED	129
		#5e 180BP_5S DNA FISH – FISH SIGNALS	dataset-5016	SEGMENTATION	CY5 THRESHOLD WATERSHED	159
#6 5S DNA FISH	Confocal	#6a SINGLE DNA FISH – RAW	dataset-5019	RAW	DAPI CROP	80
		#6a SINGLE DNA FISH – RAW	dataset-5019	RAW	CY3 CROP	80
		#6b SINGLE DNA FISH – GIFT SEGMENTED	dataset-5021	SEGMENTATION	GIFT WRAPPING	80
		#6 c SINGLE DNA FISH – FISH SIGNALS	dataset-5022	SEGMENTATION	CY3 THRESHOLD WATERSHED	75

Six types of image datasets (Dataset names) gained from wide-field or confocal microscopy (Acquisition systems) were stored as six main directories at OMERO-FSU under the name IDP3006_Dubos-Desset_2020. For each dataset, images were organized in acquisition, autocrop, raw and segmented sub-directories and can be directly accessed using the web link included into Table 1 (Link). OMERO allows to screen for key-value pairs (Key and value filters). Number of images are indicated in the last column. The six datasets and their image processing represent a total of 7,313 images.