uu-cellbiology / comdet

ImageJ plugin detecting and colocalizing particles of given size (vesicles, dots, etc on biological microscopy images)

ComDet

This is open-source ImageJ plugin for finding and/or analyzing colocalization of bright intensity spots (particles, vesicles, comets, dots, etc) in images with heterogeneous background (microscopy, astronomy, engineering, etc).

For description and manual refer to Wiki page.
Main topics:

• How to install plugin
• How to use plugin (Text Tutorial)
• How does detection work?
• How to cite plugin?

Developed in Cell Biology group of Utrecht University. E-mail for any questions.

comdet's Issues

Dual channel image not registered

Hi there

I'm trying to detect two sets of vesicles in a dual channel image for colocalization, but when running your plugin only one channel is registered. Any suggestions on how to fix this?

Exception in thread "JavaFX Application Thread" java.lang.NoClassDefFoundError: jaolho/data/lma/implementations/JAMAMatrix

Good evening,

I am trying to use your code and I got this exception on this function:

public static double estimateSigma(int[] img, ConnCompProperties roi, double[] pos, int width, double initGuess){
Gauss2D g2d = new Gauss2D();
double[][] dataXY = getData(img, roi, width);
double[] theta = getInitParameters(dataXY, pos, initGuess);
LMA lma = new LMA(g2d, theta, dataXY);
lma.fit();
System.out.println("Iteration : " + lma.iterationCount);
System.out.println("chi2 : " + lma.chi2);
System.out.println("Theta vector : ["
+ DoubleStr.double2str(lma.parameters[0]) + ", " /*
* The array of fit parameters (a.k.a, the a-vector).
*/
+ DoubleStr.double2str(lma.parameters[1]) + ", "
+ DoubleStr.double2str(lma.parameters[2]) + ", "
+ DoubleStr.double2str(lma.parameters[3]) + ", "
+ DoubleStr.double2str(lma.parameters[4]) + ", "
+ DoubleStr.double2str(lma.parameters[5]) );

    double sigma = (lma.parameters[3]+lma.parameters[4])/2.0;
    return sigma;
}

I am thinking there may be any incompatibility in the java version or the jars. I am using java 8.

Thank you very much! Any help will be appreciated

Round/oval shapes?

Love this plugin. It's easily the best object based co localization I've found. I noticed on GitHub and in your code that it may be possible to do round shapes for particle detection. Will this be forthcoming? Would be great to have a way to do circularity cutoffs so that it's easier to detect common structures, like nuclei.

Thanks again for the fantastic work

Can we select some detection parameters separately for each channel?

Hi,
I use ComDet a lot, and it's a great plugin!
However, I wish there was a modification of this plugin, and I wonder if that is possible.
So when I run ComDet for a two-channel image, I have the options for checking 'Include larger particles?' and 'Segment larger particles (slow)?'.
I hope I can adjust these two options separately for each channel.
Because checking these options for one channel may work well (more precise detection of spots as I want), but not for the other channel.
I look forward to your opinion.
Thank you very much.
Best,
Jiseok

Can we make ComDet run automatically for multiple images open?

Hi,
I am using ComDet frequently and it is so useful to me!
I was wondering, is there a way to make ComDet run automatically for multiple images open, once the parameters are set?
For my project, I need to run ComDet repeatedly for many serial images, and copy paste the results to excel each time.
However, sometimes I need to adjust some detection parameters to make the detection better, and then I have to repeat running ComDet from the beginning with the new adjusted parameter.
Do you think there's a way to do this more easily?
I look forward to your opinion.
Thank you very much!
Best,
Jiseok

Prebuild version

Hi I'm looking to install ComDet but seem to be struggling to build it myself. Is there a prebuilt image I can download from GitHub? (I see you have an actions workflow, perhaps the final JAR file can be added to the release?)

Cheers

Plugin not properly scriptable(?)

While helping my girlfriend out with a few python scripting things from within FIJI and reading the source of your plugin I found that the run(String arg) function in the Detect_Particles class completely ignores the arguments given in the arg string. This prevents the plugin from being used in a script properly as one has to manually click through the dialogs to provide the plugin with the arguments required for it to run. Is this by design because you're supposed to script in some other way or just something you've not gotten around to implementing because you haven't needed it yourself yet?

https://github.com/ekatrukha/ComDet/blob/6ab9b177cd2372d5347ab9e4dbc979e9ea149a97/src/main/java/fiji/plugin/ComDet/Detect_Particles.java#L58

Python version available?

Hello team, thanks for this repo! I was wondering if a python version of this script is available, where I can read in my image and extract bounding boxes or even a labelled image having the detected dots.
Thanks!