Can the "Record" option work for a plugin ?

[Wizel]

Hello,

I'm totally new to imageJ.
I need to count red blood cells inside microfluidic channels.
The images I'm using are in stacks (the format is called multipages TIFF) and look like this. The little white dots are the RCBs.

For now I'm using the ITCN plugin to count the RBCs. It works great even when the RBCs are in contact. But this plugin only work on a single slice and not on the entire stack.
So I'm doing each image on by one like this:
-I open my stack on the first image
-I select the ROI where I need to count the RBCs
-I start the plugin, enter the parameters and click ok
-The result is displayed, I write down the number of RBCs on a spreadsheet.
-Then I go to the second image of my stack
-I need to close and reopen the plugin
-And repeat everything from the beginning for each images and each ROIs.... It's really painful.



That's why I want to write a macro which is going to do it automatically. I want to use the record option (cause it seem easy) . But this option do not record when I go to the next slice of my stack and do not record my actions in the ITCN plugin.
So how to do that ?

Thank you.

[Nathaniel Ryckman]

You will have to look at the source for the ITCN and then create a plugin using Java. This task may or may not be simple, depending on how the "Center for Bio-Image Informatics" designed the ITCN plugin.

You can't run the ITCN as a macro according to my Google search of someone else's Google search:

"We do have a RunImageJ module in CellProfiler which is capable of running ImageJ commands or macros. However, after some Googling, I found that the plugin is not configured in such a way to permit running it as a macro (which RunImageJ would need). " May 18 2011

http://www.cellprofiler.org/forum/viewtopic.php?f=14&t=1235

Wizel wrote

Hello,

I'm totally new to imageJ.
I need to count red blood cells inside microfluidic channels.
The images I'm using are in stacks (the format is called multipages TIFF) and look like this. The little white dots are the RCBs.

For now I'm using the ITCN plugin to count the RBCs. It works great even when the RBCs are in contact. But this plugin only work on a single slice and not on the entire stack.
So I'm doing each image on by one like this:
-I open my stack on the first image
-I select the ROI where I need to count the RBCs
-I start the plugin, enter the parameters and click ok
-The result is displayed, I write down the number of RBCs on a spreadsheet.
-Then I go to the second image of my stack
-I need to close and reopen the plugin
-And repeat everything from the beginning for each images and each ROIs.... It's really painful.



That's why I want to write a macro which is going to do it automatically. I want to use the record option (cause it seem easy) . But this option do not record when I go to the next slice of my stack and do not record my actions in the ITCN plugin.
So how to do that ?

Thank you.

[Wizel]

Oh Thats bad for me.
I don't have time to learn Java, learn how the plugin works and modifying it in 10 days.

I guess I'll continue to do by hand...


Thank you for your fast reply !