Up: Component summary
Up: Component summary
Component
CellProfilerRuns 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, |
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