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CellProfiler

Runs a pipeline in CellProfiler, for a folder or several folders of images.

You have to edit an existing CellProfiler pipeline in order to use this component. Keywords in the command are as follows: @in1@ .. @in9@ refer to input folders in corresponding input ports. @out1@ .. @out9@ refer to the output folders. Parameters may be used with keywords @param1@ .. @param9@

Install CellProfiler from http://cellprofiler.org/ . Installation on Linux: http://cellprofiler.org/wiki/index.php/CP2.0_on_Linux . The CellProfiler can be installed in the bundle lib folder, or in a user defined location with the given parameter.

NOTE: Handling errors that happened in CellProfiler are difficult to interpret in Anduril. Make sure that your pipeline works. Also, if the filenames / full path contains commas (,) you might get errors.

Version 1.0
Bundle anima
Categories Image Processing
Authors Ville Rantanen (ville.rantanen@helsinki.fi)
Issue tracker View/Report issues
Requires bash ; imagemagick (DEB) ; CellProfiler
Source files component.xml cellprofiler.sh
Usage Example with default values

Inputs

Name Type Mandatory Description
pipeline TextFile Mandatory Pipeline file (see examples)
in1 ImageList Mandatory Input folder of images, also the default input folder
in2 ImageList Optional Input folder of images
in3 ImageList Optional Input folder of images
in4 ImageList Optional Input folder of images
in5 ImageList Optional Input folder of images
in6 ImageList Optional Input folder of images
in7 ImageList Optional Input folder of images
in8 ImageList Optional Input folder of images
in9 ImageList Optional Input folder of images

Outputs

Name Type Description
out1 BinaryFolder Output folder 1, also the default output folder
out2 BinaryFolder Output folder 2
out3 BinaryFolder Output folder 3
out4 BinaryFolder Output folder 4
out5 BinaryFolder Output folder 5
out6 BinaryFolder Output folder 6
out7 BinaryFolder Output folder 7
out8 BinaryFolder Output folder 8
out9 BinaryFolder Output folder 9
pipelineDebug TextFile Pipeline file with replaced content

Parameters

Name Type Default Description
param1 string "" custom parameter param1
param2 string "" custom parameter param2
param3 string "" custom parameter param3
param4 string "" custom parameter param4
param5 string "" custom parameter param5
param6 string "" custom parameter param6
param7 string "" custom parameter param7
param8 string "" custom parameter param8
param9 string "" custom parameter param9
path string "../../lib/CellProfiler/" Location of CellProfiler.py.

Test cases

Test case Parameters IN
pipeline
IN
in1
IN
in2
IN
in3
IN
in4
IN
in5
IN
in6
IN
in7
IN
in8
IN
in9
OUT
out1
OUT
out2
OUT
out3
OUT
out4
OUT
out5
OUT
out6
OUT
out7
OUT
out8
OUT
out9
OUT
pipelineDebug
case1_dapi_segment properties pipeline in1 (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing)

param1=200,
metadata.timeout=0


Generated 2018-12-18 07:42:13 by Anduril 2.0.0