These are chat archives for fiji/fiji

Nov 2018
João Pereira
Nov 12 2018 01:24 UTC
Hello, I am new to imagej development and I would like to see if there is any example of a Fiji plugin that would allow me to open an image and display it. My objective at this point is to open a stack image in a window and duplicate one of the channels and show the original and the duplicated in the same window.
Curtis Rueden
Nov 12 2018 01:29 UTC
@joaopapereira Are you trying to write a script that does that, to repeat those steps more easily? You can try the Macro Recorder for an easy way to do that.
I suggest you post at if you have more detailed questions about how to do specific things.
João Pereira
Nov 12 2018 02:26 UTC
@ctrueden I would like to have a bit more control over the images after. So my idea is to be able to open the channel twice and control one of the image. I cannot use the macro recorder because I need to have a automation in the beginning, then manual intervention to change some settings by hand and then apply some other automated steps. So I was thinking in developping a plugin that would allow me to do this "pipeline" of steps
Curtis Rueden
Nov 12 2018 15:12 UTC
@joaopapereira I would encourage you to write a script, rather than a plugin. Scripts have full access to the entire API. The syntax is more succinct, and you can use script parameters.
As for the macro recorder, it is just a way to learn the API calls. Set it to JavaScript and you can see the non-macro way of calling into ImageJ. You can write semi-manual scripts that stop and wait for user input, etc.
Nov 12 2018 15:15 UTC
Hello, I am new to Fiji and I need to find a method to recognize the nearest particle from one stack of images to another. I would appreciate any ideas please :)
I used the plugin 3D Object Counter and got an object map and centroid map but I don't know how to continue, I'm thinking maybe Image calculator?
Jean-Yves Tinevez
Nov 12 2018 15:56 UTC
@beatriz11248456_twitter is a good place to post such questions. Here we typically discuss development issues.