HTPheno setup problem

Hi there
I have installed HTPheno plugin to ImageJ (Version 1.50i) and have viewed the tutorials at the site However I have been unable to begin to customise the .csv file templates for my images and classes/areas of interest. For when I click and open the “config_Color2class_top.csv” (or side.csv), a Results window appears (Left image) rather than the template window as in the first set-up tutorial (Right image).

Left image. My “config_Color2class_top.csv” display file window. Showing results of pre-existing classes.
Right image. Window that should appear when “config_Color2class_top.csv” is opened (From setup tutorial).

Assistance with this issue would be much appreciated.

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Welcome to the forum, @miket!

This might be caused by a recent change in how ImageJ 1.x handles csv files. From the release notes:

  • 1.51m 30 April 2017
  • […]
  • Changed the default extension when saving tables from “.xls” to “.csv” (coma-separated values) and added support for opening and saving tables in “.tsv” (tab-delimited values) format.

You should be able to work around the issue by either:

  • opening the file in the script editor (if you use the Fiji distribution, the currently recommended way of using ImageJ), or
  • renaming the file(s) to .txt and then opening them.

I don’t think the original authors are active on this forum, so I invited Anja Hartmann to this forum topic, as they might want to update their plugin documentation.

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Thanks Jan,
This has helped a lot with making some progress. I’ve opened the files in notepad and edited them. This has enabled me to define classes and execute the calibrate image process according to the defined classes. However when running the application on a test image just exceptions result. I will need to try your next advice regarding installing Fiji and then using the script editor to assist with troubleshooting.

Good idea informing the authors.


Can you post the exact exceptions? This will certainly help troubleshooting.

Hi Jan
Here’s the exception result to date.