ICY spot detector and tracking in 3D

Hello everyone,

I am new to ICY (started working with it after the excellent webinar in the NEUBIAS home academy) and I am trying to set up a workflow to detect and track spots over time in 3D.
Is that possible with the “Spot Detector” + “Spot Tracking” plug-ins in ICY?

I was able to detect spots and load them into the tracking module, but I am not sure if the results I got were calculated in 3D. The input is a single channel z-stack over 6 time points; I applied a Median 3D and a LocalMaximum Filter:

Thanks in advance!!
Best, Hanna

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Hi @Nele09

You can indeed use Spot Detector then Spot Tracking to do 3D spot tracking.
If you use a 3D stack the spots should be detected (and so tracked) in 3D.
Can you describe a bit more your current workflow ?
You have this example workflow (Protocol) in Icy which does Spot tracking then motion analysis.
You can open it in Icy just typing ‘motion’ keyword in the top search bar (you should quickly find the protocol).

Best,

– Stephane

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Hi Stephane,

thanks for the answer! I have downloaded the protocol you linked and I’m going to try it out now.

So far my workflow was a 3D median filter, followed by the local maxima filter and then the spot detection (with the default settings and a size filter) and spot tracking.
I have to play around with the settings a bit more to get only the spots I want, but otherwise it is working well.

I’ll cry for help again, if I run into more troubles. :upside_down_face:
But again, thanks for the feedback!

Cheers, Hanna

Hi Hanna,

You’re welcome ! Depending your images you don’t necessary need to filter before using Spot Detector as Spot Detector is made to detect spot in noisy condition. So i recommend you to always try on raw data first, then try with filtering to see if that really improves the result :wink:

Good luck !

Best,

– Stephane

Hi Stephane,

I will try it without the filter, thanks for the input.

All the best,
Hanna