basic pixelated STEM.txt

Minimum information for a quantitative pixelated STEM file

suitable NeXus application definition: Extension/instantiation of NXscan http://download.nexusformat.org/doc/html/classes/applications/NXscan.html

NXinstrument http://download.nexusformat.org/doc/html/classes/base_classes/NXinstrument.html
	Illumination --> Should probably get an STEM-specific base class. NXsource doesn't quite fit
		Beam current 
		Beam energy
		Convergence angle
		Spot size
		Optionally/advanced
			Illuminating wave front -- deal with that later?
			Probe image?

	Scanning --> Might need a new base class? EMs can both shift the beam and translate the sample, while synchrotrons and neutron sources usually only move the sample afaik
		Option 1: parallelogram scan or rectangular scan
			corner 1 (x, y) (start)
			corner 2 (x, y) (end of first line)
			corner 3 (x, y) (only distance if rectangular, otherwise overdetermined)
			pixels per line
			pixels per column
			
		Option 2: non-rectangular scan
			pos_x (list)
			pos_y (list)
			
		Scan rate or start/stop times
			
	Detector --> NXDetector http://download.nexusformat.org/doc/html/classes/base_classes/NXdetector.html
		x-pixels
		y-pixels
		physical size (x, y)
		bit depth / number format
		make & model (not strictly necessary, but recommended)
		gain curve -- link numerical detector readout to electron dose
		
	Virtual detectors
		Each with mask and reduced data set. Users can add more
		BF
		ADF
		HAADF
		Sectors?
	
	Projection
		camera length --> links pixel position to scattering angle (NXtransformations? http://download.nexusformat.org/doc/html/classes/base_classes/NXtransformations.html)
	
Sample (not strictly necessary, but data would be pretty meaningless without that info) NXsample http://download.nexusformat.org/doc/html/classes/base_classes/NXsample.html
	ID
	thickness (not strictly necessary, but recommended)
	Composition (optional, but very helpful)
	Crystal unit cell/structure/space group (optional, but very helpful)
	Sample surface expressed as crystal plane (optional, but very helpful)
	Orientation relative to beam (optional, but very helpful)
	

Drift corrections (optional, but often necessary) --> New base class?
	Several entries possible
		correction_x (list) -- or better pos_x?
		correction_y (list) -- or better pos_y?