Providing input images to "Spot tracking with excel export" protocol in headless mode

[Ben Lansdell]

Hi, 

thanks for providing this protocol, it's a useful example to have. 

I'm trying to figure out how to provide a list of input images to the protocol so it runs entirely from the command line. Currently I run the protocol as so:

java -jar icy.jar --headless --execute plugins.adufour.protocols.Protocols protocol=./spottracking.xml

I modified the protocol to start with a 'Files to Sequence' block to input my images. When editing the protocol, I can select a list of files, and can then run the protocol from the GUI. My choice of files doesn't appear to be saved in the .xml file, however, so then running the protocol in the command line doesn't load the images I want. 

Could you provide advice on either: 

1) which command line arguments I could provide to input the images? 

2) how I can modify the .xml file to specify the input images. 

I've tried, for 2), adding a 'value' field to the 'input' variable of the FilesToSequence block with the list of files I want. This works for a single image, but I can't figure out the format required to input a list of files. The particle tracker returns an error with just a single input image.

Thank you.

Regards,

Ben

[Stephane]

Hi Ben,

Protocols plugin allow since version 3.0 to provide input parameters from command line which is exactly what you need here.
Alexandre will enrich the plugin documentation soon to explain how use it.
I will let you know when documentation will be updated :)

Best,

- Stephane

[Alexandre Dufour]

Hi Ben, 

I’ve updated the documentation on the plugin’s web page (thanks to Stephane’s screenshots): http://icy.bioimageanalysis.org/plugin/Protocols

Regarding the issue you mentioned, the “Files to sequence” block should now properly save the selected files (this issue was fixed a few weeks ago). Make sure you have the latest version of Icy and its plugins and let us know if the issue remains.

Alexandre