Revvity Harmony Options ( IAHarmonyOptions )

Parameters:

Name	Short Name	Type	Description
Apply background flatfield correction	backgroundflatfield	boolean	Subtract inhomogeneous background based on the polynomial function supplied by metadata. This is performed on the frame basis, before stitching.
Mean background type	bgtype	string	The background flat field correction will use mean background determined by this method in each frame or given by metadata to scale the flat field correction polynomial.
Mean background value (intensity or percentile)	bgvalue	real	Value corresponding to the above selected mean background determination type. Not in use when selecting metadata above.
Zero background	zerobackground	boolean	The default handlig by Revvity is leaving the mean background unchanged by the flatfield correction. Instead here the faltfield can be plainly subtracted, ideally resulting close to zero background.
Apply foreground flatfield correction	foregroundflatfield	boolean	Normalize inhomogeneous illumination based on the polynomial function supplied by metadata. This is performed on the frame basis, after background subtraction and before stitching.
Apply high pass filter on bright field	filterbrightfield	boolean	Uneven background is removed by spatial filtering in the absence of flat field correction. This is performed on the frame basis, before stitching. Alternatively use the spatial filter setting of the Multi-Dimensional Open Dialog.
High pass filter cut on (pixels)	cuton	real	Cuton value for a high pass Butterworth filter (order=1.3). A larger cut on value provides stronger filtering effect.
Stitch tiles	stitching	boolean	Stitching is performed after background and illumination corrections, using image metadata. The way of stitching may be overridden by changing paramaeters in the Stitching tab of the Multi-Dimensional Open Dialog.
Manual configuration of stitching	manualstitch	boolean	This loader will not override the Stitching tab of the Multi-Dimensional Open Dialog.
Use skewcrop for stitching	skewcrop	boolean	Use Revvity`s skewcrop method to account for camera angle, improving registration of objects across frames, but causing blank edges.
Fade tiles [not implemented]	smoothstitch	string	Smooth stitching is achieved by fading tiles at the edges.
Inpaint empty areas	inpaint	boolean	Areas not covered by tiles will be inpainted (guessed) to prevent blank/black edges when using skewcrop.
Experiments are shown as	naming	string	Experiments will be shown by this name instead of GUIDs.

Description:

This function provides options how to load Revvity harmony data sets.
Flatfield corrections and image filtering are applied before stitching. Stitching follows coordinates in metadata, or optionally configure it in the Stitching Tab. No image registration is perfomed. Stiched images may not fill the entire large image area, leaving blank edges due to correction for camera angle. Turn off skewcrop or inpaint blank edges if this causes problems in analysis. Correction for angle and pixel shift differences between channels for multi-camera systems is not yet implemented.