imagej / imagej/imagej-server

How do I run an ijm script?

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#43 0 comments 0 reactions 0 assignees View on GitHub
Dominant language
Java
Stars
40
Forks
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Description

I'm attempting to run an ijm script by changing the example that runs a python script.

The script I'm attempting to run is as follows:

```
run("Set Scale...", "distance=4.585 known=1 pixel=1 unit=µm");
setAutoThreshold("MaxEntropy dark");
setOption("BlackBackground", true);
run("Convert to Mask");
run("Despeckle");
run("Watershed");
run("Analyze Particles...", "size=16-Infinity circularity=0.50-1.00 display exclude summarize");
```

I tried setting `language` to `ijm` and `in1` to the script but that caused an error. I tried escaping the quotes, parentheses, and replacing the newlines with `\n` and that still caused an error. I tried changing `in1` to be `script` and removing `in2` and I'm still seeing errors.

Any help would be appreciated.

Contributor guide

No contributing guide indexed for this repository

Research direction

The issue includes an IJM script and describes failed attempts involving language, in1, and in2, but names no repository file, endpoint, or complete failing request. Start by comparing the request used for the Python example with the information provided here. Done means establishing the correct way to submit this script or documenting the missing request details needed to diagnose it.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
api
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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