Image processing pipelines in Image Analyst MKII
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Neurite outgrowth assay

Parameters:
Name # Type Description
Channel number of neurite stain 1 integer The first linked image window with matching channel number will be invoked.
Channel number of nuclear stain 2 integer The first linked image window with matching channel number will be invoked.
Number of tiles in x 3 integer The image consists of this number of equal sized tiles in x dimension.
Number of tiles in y 4 integer The image consists of this number of equal sized tiles in y dimension.
Approximate nucleus diameter 5 integer Diameter of the nucleus in pixels. A range of cell size from about half to double will be selected.
Debris cutoff for nuclei (percentile of reference) 6 real Brighter details of the image than this will be ignored
Minimum nucleus fluorescence (%) 7 real Cells dimmer than this will be rejected. Increase this value if debris dimmer than the cells is detected.
High pass filter for neurites Cut On ω (pixels) 8 real The amount of background suppression by the high pass filter. Typically 50-200.
Debris cutoff for neurites (percentile) 9 real Brighter details of the image than this will be ignored. Decrease this value if bright debris results wrong scaling of nuclei.
Minimum neurite stain fluorescence (%) 10 real Cells dimmer than this in filtered rescaled images will be rejected. Increase this value if debris dimmer than the cells is detected.
Description:
Calculates average skeletal length of fine processes around cells.
The output is the sum of all processes in pixels length as "channel 1" and the nucleus count in "channel 2". Calculate average neurite length in pixels/cell by dividing these values.
The pipeline was designed the detect fluorescence neurites over high and uneven background, and to work in microplates in an unsupervised manner, where cell densities may substantially vary well to well.
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.
Internal version: v3.6