FIJI (ImageJ): Counting Objects in a Grid

Learn how to use FIJI (ImageJ) to count and measure objects inside a grid. This video shows how to do this step-by-step or by using a macro. The macro used in this tutorial was adapted from the image.sc forum (written by Rob Lees).
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[@jonascampos1895]

Great one Johana!👌

[@宋放]

Hi Johanna! Thank you so much for your informative and helpful videos. I have learned a lot!🥰 Could I ask you a question? I am working on cell aggregates(spheroids). After staining the cell nuclei, I got the 3D fluroscent stacks by confocal microscope. I need to count the cell number within the whole cell aggregates by 3D objects counter. But the noise of the picture is a little bit high, and the fluorescence of different cells is sometime connected together. I try to deconvolution first, and then use weka segmentation. But either the fluorescence of multiple cells is connected, or cells with weak fluorescence are ignored. Is there any way to solve this? Thank you so much!

[@宋放]

Sorry, the first sentence is mistyped.

[@johanna.m.dela-cruz]

Thanks, I’m glad the tutorials are helpful. Did you try pre-processing your images first to get rid of the noise? Have you tried using watershed to separate touching objects? If you are counting cells, you could also just try finding maxima.

[@宋放]

Thank you for your kind reply@@johanna.m.dela-cruz . For getting rid of the noise, I only use deconvoltion, would it be better combine like subtract background with deconvolution? I use process>binary>water shed, but I think it's still not good enough. Is there any advanced watershed method? Thank you so much again!

[@johanna.m.dela-cruz]

@@宋放 It is usually better to subtract the background signal from the stack in order to generate a useful measured PSF for deconvolution. You can try 3D Watershed in 3D ImageJ Suite. I haven't tested this yet, but there is another plugin for interactive watershedding: imagej.net/plugins/interactive-watershed. This gives me an idea for a new topic for my tutorial series. 🙂

[@宋放]

Thank you so much for helping me🥰@@johanna.m.dela-cruz

[@solokmalang]

Hi Johana, Thank you so much for a great video. I try to use this method to count the number of cells in several grids in my images. I want to ask a question, It is possible to get the script from you?.

[@johanna.m.dela-cruz]

Hi @solokmalang. Yes, send me an email. Thanks for watching.