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SegmentFiji

Produces binary mask images, segmenting the input images using Fiji. For method selection, see: http://fiji.sc/Auto_Threshold. Append method name with " dark" to invert image first.

Version 0.1
Bundle anima
Categories
Authors Miko Valori (miko.valori@helsinki.fi)
Issue tracker View/Report issues
Requires Fiji
Source files component.xml fijistart.py fijithreshold.sh
Usage Example with default values

Inputs

Name Type Mandatory Description
in ImageList Mandatory Grayscale input images to be segmented.

Outputs

Name Type Description
mask ImageList Generated masks as .png files
perimeter ImageList Generated perimeters as .png files

Parameters

Name Type Default Description
corr float 1 Correction coefficient for calculated threshold level
display boolean false Set to true to use the current DISPLAY. When false, tries to send screen to Xvfb (if installed), use to debug etc..
method string "Otsu" Method used for setting segmentation threshold

Test cases

Test case Parameters IN
in
OUT
mask
OUT
perimeter
case1 properties in mask perimeter

corr=0.4,
metadata.timeout=30


Generated 2018-12-11 07:42:05 by Anduril 2.0.0