Measure mitochondrial MEAN shape parameters

Parameters:

Name	#	Type	Description
Largest mitochondrion size (width in pixels)	1	real	Give an approximate width of the largest mitochondria. This value controls the high pass filter to suppress larger than mitochondrial details. It does not act as a classifier for mitochondria, so slightly larger objects will also appear in the image. Decrease this value if smaller mitochondria are lost during segmentation. Increase this value if noise passes through from background.
Sensitivity (top range scaling, percentile)	2	real	A percentile value, typically between 95-99.99 percentile. Decrease this value to increase sensitivity, if dimmer mitochondria are lost during analysis, or if bright debris is present in the image. Increase this value if noise passes through from background.
Minimum size (area, pixels)	3	integer	Minimum size of mitochondria to detect. This is an object classifier, smaller objects than the specified size will be removed. Decrease this value if smaller mitochondria are lost during the analysis. Increase this value if noise passes through from background.
Morphological parameter	4	string	Select the morphological parameter of interest: "number", "area", "perimeter", "diameter", "filament length", "branch points", "shape factor", "fiber length", "fiber breadth", "distance from ROI". Note: to measure distance from ROI, draw an ROI before running the pipeline.
Place positions into columns	5	boolean	This parameter affects how the data is printed into the spreadsheet. When multi stage position recordings are analyzed, time courses from consecutive positions will appear next to each other if yes, rather than appending results below the data corresponding the previous position.

Description:

Mitochondrial profiles are detected by uniform (global) thresholding in high pass filtered and rescaled images. The uniform threshold level-based simple segmentation used here prevents objects breaking up in contrast to the seed-based watershed segmentation used for nuclei segmentation. This is the core algorithm of the mitochondria:cytosol volume fractionator. The chosen morphological parameter as the mean of all mitochondria is transferred to the Excel Data Window.

See corresponding protocol at: http://help.imageanalyst.net/protocols_morphological_properties_of_mitochondria.html

Keywords: mitochondrial fission, mitochondrial fusion, mitochondrial fragmentation, mitochondrial swelling, mitochondrial dynamics, mitochondrial shape change, apoptosis, mitochondrial permeability pore opening

Version history:
V2:
Updated description