Mechanical Testing & Topography (Atomic Force Microscopy)

	A	B	C	D	E
1	ALSDA Assay Metadata, Image, Outcome Measure Configuration for AFM	Mechanical Testing & Topography (Atomic Force Microscopy)			RS started 8/2/23; XP edited 06/24 (with 2 PI assessments) ; XP edited with TA's assessments 06/24
2	File Folders will contain: Study Metadata File, .log file, Force-displacement images, raw mechanics tabular data, processed tabular data, phase image	Measurement: Mechanical Tests Ontology: http://purl.bioontology.org/ontology/MESH/D000083522
3	Supporting Literature: Necas and Klapetek 2012; Schulze et al, 2021; Wu et al 2018, Schillers et al 2017, Vahabi et al 2013, Cappella and Dietler 1999, Joshi et al 2022, Verbelen et al 2006, Giessibl 2003, Walters et al 1996, Akhatova et al 2022, Asgari et al 2022, Payam and Passian 2023, Mull and Kreplak 2022	Technology: Microscopy, Atomic Force Ontology: http://purl.bioontology.org/ontology/MESH/D018625
4
5	Instructions: Adapt behavior template to the assay. Use the Configuration Headings to organize information according to the description of the heading in the Notes. Feel free to add, delete, or modify rows. If your parameter can be described using existing wording, preserve the existing wording. If there are similar parameters that need to be distinguished, try to use the parameter wording and add modifying words. Use the MINIMUM metadata parameters necessary to make the data REUSABLE, rather than trying to exactly REPLICATE all conditions under which the assay was performed. Parameters are to be used for screening data sets to determine if they match the conditions a user sets for comparison to other data sets, or for meta-analysis of the effect of a parameter on the dependent variable data.
6
7	Parameter	Example Value	Data Type	Unit	Notes
8	ALSDA Assay Metadata Configuration for AFM
9	AFM Hardware Settings and Qualities
10	AFM Model (manufacturer, model number)	e.g. Veeco Metrology Group (currently Broker Nanosurfaces, Nanoscope IV Multimode AFM, NanoWizard V for bio work in lfuid	String
11	AFM Probe Used	e.g. qp-BioAC, SNL-10, MLCT-Bio, SAA-SPH-1UM	String
12	Does the probe have a tip or is it tipless?	e.g. Tip or Tipless (with 5 um diameter silica sphere), or cell as probe on the tip	String
13	AFM Tip or Sphere material (and shape?)	e.g. Silicon or silicon nitride, reflective gold	String
14	AFM Cantilever shape	e.g. Parabaloid, spherical, triangular	String
15	Spring Constant	e.g. 0.01 Nm^-1	Double
16	AFM Tip Radius	e.g. 10 nm	Double
17	Cantilever Length	e.g. 100 nm	Double
18	AFM Operation Settings
19	Mode of Operation	e.g. Lateral force microscopy, Nanoindentation mode, Dynamic force\intermittement contact (tapping mode?), Force modulation, Phase/Height imaging, Force spectroscopy, force volume mapping, or other	String
20	Imaging Temperature	e.g. 20 degrees Celcius	Double	Celsius
21	Minimum Applied Force	e.g. 500 nN	Double	nN
22	Spring Constant	e.g. 2.7 N/m	Double	N/m
23	Scanning Rate (Frequency)	e.g. 0.8-0.9 kHz	Double	kHz
24	Scanning Force	e.g. 1-2 nN	Double	nN
25	Indentation Rates	e.g. 0.1, 0.5, 1, 2, and 5 μm s^-1	String
26	Test Attributes (Tension, compression, 3pt, 4pt)	e.g. 3pt	String		Microindentation AFM should only be used in compression loading
27	Control Mode (Load or Displacement Control)	e.g. Load Control	String
28	Is this test monotonic or fatigue	e.g. monotonic	String
29	Displacement Rate (Rate of applied load or displacement)	e.g. 0.01 mm/s	Double	um/s
30	Scans of Sample	e.g. 100 um	Double
31	AFM Sample Settings and Qualities
32	Technique	e.g. AM-AFM, EFM, KFM, MRM, Biomodal AFM, FMM, AFAM, UAFM	String
33	Sample	e.g. Collagen, live cells, live tissue	String
34	Approximate Material Dimensions	e.g. 25 sq nm	Double
35	Substrate	e.g. mica, glass, silicon oxide, Isopore polycarbonate membranes, elastic silicon membrane or petri dish coated with matrix proteins, petri dish, etc	String
36	Immobilization Method	e.g. mechanical trapping, adherent cells to matrix, mechanical immobilization	String
37	Sample Medium	e.g. Aqeous , In Air, or other (5uL of solution), cell culture media,	String
38	Sample Surface Area	e.g. 400 × 400 nm2	Double
39	Section Thickness	e.g. 20 nm, cell size 10-100 micron, tissue few mm length	Double
40	AFM Data Aquisition
41	Image Taken	e.g. Height, Deflection, and or Phase	String
42	Amount of Images Taken	e.g. 50	Integer
43	Image Resolution	e.g. 1024 x 1024px	String	px
44	Scan Region	e.g. 50 um x 50 um	String
45	Alignment or Location along sample	e.g. corners and center	String
46	Image Processing Software	e.g. Nanoscope Analysis v3.0, JPK Data Processing Software, Gwyddion, Fityk	String
47	Force curves	string of numbers - deflection vs indentation	String		obtained from force spectroscopy measurements (approach curve used for stiffness measuments, retraction for adhesion measurements)
48	Outcome/Dependent Variable Measures for AFM - Standardly Used Nomenclature & Units
49	Adhesion (nN)
50	Elastic Modulus (KPa)
51	DMT Modulus (MPa)
52	Deformation or Indentation Depth (nm)
53	Elastic_modulus_E_Newtons_per_millimeter_squared
54	Toughness_Newtons_per_millimeter_squared
55	Max_Stress_s_Newtons_per_millimeter_squared
56	Fatigue Strength
57	Mechanical Properties
58	Stiffness_N_per_mm_Newtons_per_millimeter
59	Work_to_fracture_Nmm_Newtons_times_millimeters
60	Post-yield_displacement_millimeters
61	Maximum_Load_N_Newtons
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