4DN-OME_Microscopy Metadata_2019-3-22_v00-11

	A	B	C	D	E	F	G	H	I	J	K
1									-- required metadata --
2	Old ID	New ID	Name	Description	Example	Example Labelling	PSFj calibration	detector calibration	experiment/sample	specifications	settings
3	D1	1	Documentation	Reporting qualitative effects without quantification	Transfection control, viability assay	FISH, Immuno Fluorescence	recommended annually (not required)	not recommended	- experiment, sample and image name, date and description - experimenter name	-microscope manufacturer, name and type -light source type -objective magnification and NA	- dimension order - physical pixel size x and y, physical z distance - time increment - optovar magnification - channel name, color and acquisition mode
4	D2	2	Simple Quantification	Identification of non-refractive limited objects followed by basic feature extraction and statistical analysis	Counting of cells and nuclei, expression level measurements	FISH, Immuno Fluorescence	recommended quarterly (not required)	not recommended	- mounting medium	-microscope model -light source name, description, manufacturer, model, wavelenght -objective manufacturer, model, and correction -detector type, manufacturer, model, and relay magnification	- exposure time - immersion medium name and nominal refractive index - image X, Y, Z, C and T size - channel illumination type, contrast method, fluorophore, - filter manufacturer and name
5	A1	3	Advanced Quantification	Identification and localization of refraction-limited particles, super-resolution microscopy	Measurement of distances, co-localization studies	Single Molecule FISH or Immuno Fluorescene	required quarterly (submit report)	recommended	- imaging temperature	- detailed light source, light source coupling, light path, channel and detector specification & settings - detailed light path specifications & settings - light source power output and detector calibration results
6	A2	4	Life Cells Imaging	Tracking of intracellular dynamics	Particle tracking, live cell expression level measurements, limited signal, advanced processing,	CasFISH, CRISPRainbow, fluoresent protein labelling	required monthly (submit report)	highly-recommended	- imaging air pressure, humidity and CO2 percentage - mounting medium measured refractive index	- imaging standard type - light source coupling, foucusing and autofocus specification & settings - objective iris specifications - dichroic mirror and additional optics transmittance, reflectance and angles	- objective temperature - immersium medium measured refractive index
7	P	5	Virtuoso	Full reproducibility of microscopic set up and image acquisition	Development of novel unproved technology, new gold-standard, need to make sure microscopy set up can be reproduced in another laboratory	All of the above	required weekly (submit report)	highly-recommended	all the metadata specified by the data model (Figures 2 and 3) - including any novel technology-specific metrics
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100