Particle measurements in microfluidics


Hello @tinevez

i am new to image analysis. I have four images taken at different time as it move thorough the microfludics. I am trying to find fit ellipse to find major diameter. How can i do that at once.
I have uploaded my sample image.

Welcome to the ImageJ Forum!

Hi @sawrosecfc
This looks tricky at least to me. Can we see a movie of what happens?
I guess the main difficulty will arise when the cell borders touch the capillary borders.


@tinevez thank you for the reply, I don’t have a movie. I have set of images with time written over them.
I have uploaded a image with cell inside the capillary. i wanted to ask if you know

  1. Is there any way to abstract time from these image sample?
  2. second thing i wanted to do is to find the diameter as the cell in different images?

Thank you in advance for your suggestion.


Honestly going to a fully automatic process looks to me like a very complicated task.

I do not know how to reliable remove time from the images, apart from asking for the raw data, unannotated.

As for the diameter measurement, I would try to fit an ellipse on the dark contour of each cell. I don’t think that there is a plugin existing that does that. I tried to do something like this years ago, and it did not come to fruition, so you would have to code yourself. To do so I would have a function that samples the perimeter of an ellipse, and minimize the pixel intensity of the pixels that are traversed by the perimeter.

But even this is not fully automated as you need to initialize the ellipse above each cell.


To highlight the differences between two images, you can use Process > Image Calculator… to subtract your images, which might help to identify the cells. This is what I got when subtracting your first example image from the second one:


thank you for the reply


Ok i like the idea, i will try something out of it. Thanks for the suggestion.