Image processing pipelines in Image Analyst MKII
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Video or image export 1-4 channels with local background subtraction

Parameters:
Name # Type Description
Channel #1 Color (Look Up Table) 1 string Look Up Table: "Grayscale", "Red", "Green", "Blue", "Pseudocolor", "Intensity Gated Pseudocolor", "Fire", "ROI color", "Off"
Channel #2 Color (Look Up Table) 2 string Look Up Table: "Grayscale", "Red", "Green", "Blue", "Pseudocolor", "Intensity Gated Pseudocolor", "Fire", "ROI color", "Off"
Channel #3 Color (Look Up Table) 3 string Look Up Table: "Grayscale", "Red", "Green", "Blue", "Pseudocolor", "Intensity Gated Pseudocolor", "Fire", "ROI color", "Off"
Channel #4 Color (Look Up Table) 4 string Look Up Table: "Grayscale", "Red", "Green", "Blue", "Pseudocolor", "Intensity Gated Pseudocolor", "Fire", "ROI color", "Off"
Show only composite image 5 boolean Yes executes output #1, No executes output #2.
Subtract reference image background 6 boolean Yes executes output #1, No executes output #2.
Local background subtraction method 7 string The Nth output will be executed when the Nth value is selected here from a ;-separated list given below at "Possible selector values".
Rolling ball: median filter size 8 integer The median is calculated over a width x width rectangular area around each pixel of the image.
Spatial filtering: Number of tiles in x 9 integer The image consists of this number of equal sized tiles in x dimension.
Spatial filtering: Number of tiles in y 10 integer The image consists of this number of equal sized tiles in y dimension.
Spatial filtering: Largest object size (for background removal, pixels times number of tiles) 11 real Size of the object to be passed by the filtering. The pixel size must be multiplied by the number if tiles (in x or y). Objects larger than this will be removed as background. Cut on of the band pass Butterworth filter.
Global background level (Percentile) 12 real Background is calculated as frame-by-frame mean of those pixels that are the darker than this percentile of image histogram for the duration of the entire recording.
Scaling, Min percentile 13 real This percentile of the image histogram sets the intensity value where the minimum of the Look Up Table (LUT) is scaled. Use -1 to override this with fixed value set below at "Min value".
Scaling, Max percentile 14 real This percentile of the image histogram sets the intensity value where the maximum of the Look Up Table (LUT) is scaled. Use -1 to override this with fixed value set below at "Max value".
Show time stamp 15 boolean Turns on time stamps (set font in the Preferences Dialog/Misc tab).
Time stamp format 16 string Time will appear like this: "0 s", "0.0 s", "0.00 s", "0.000 s", "0000 ms", "00'00"", "00'00"00", "00h00min"
Show scale bar 17 boolean Turns on scale bar.
Scale bar unit 18 string Available units: "nm", "µm", "mm", "cm", "m".
Scale bar size 19 real Length of the scale bar in the units given above.
Export image/video 20 boolean Yes executes output #1, No executes output #2.
Export Filename 21 string
Video or Image Format 22 string Available formats: "BMPPadded", "BMP", "AVI", "JPG", "JPGPadded"
Description:
This pipeline removes inhomogeneity of background with high pass filtering, scales the image with the Look Up Table (LUT) of choice, applies time stamp, scale bar and exports in the format of choice. The tiled high pass filter can efficiently remove pattern originating from tiled imaging using wide field microscopy.
Set time stamp font in the Preferences Dialog/Misc tab.
Tiled images: the background tiling pattern is efficiently removed by spatial filtering if the recording was performed without overlap and image registration. Provide the number of tiles in x and y direction.
Note: See help on expression evaluation to set up automatic file naming.

V2:
Changed Export filename