If I want to have the same number of fluorescent spots in each image, how should I set it?

[zhangshenhe]

I can change the average number of fluorescent spots per image by setting the Simulation.emitter_av parameter. If I want to have the same number of fluorescent spots in each image, how should I set it?

[Haydnspass]

Dear @zhangshenhe
this is not possible for training when using emitters with blinking dynamics (because of the stochastic activation and lifetime). However you could change to the Static Emitter Sampling.

[zhangshenhe]

Thank you for your answer, I have another question. I set the parameter param.Simulation.intensity_mu_sig = [10000.0, 1000.0], and set an average of 25 fluorescent spots per frame. However, I often encounter spots with very low fluorescence intensity, sometimes even only around two hundred, and this seems to happen quite frequently. It appears that every image has spots with intensity less than 1000. I can't discern these spots with the naked eye. Is there a way to generate only spots with higher fluorescence intensity? Thank you once again.

[Haydnspass]

Hey @zhangshenhe ,
this is due to the way we sample emitters. We sample a photon flux and their start and lifetime. if we have say 1000 photon flux, but they are only on 1/100 of a frame this would result in 10 photons on one frame.
To change that, you could change to static etmiter sampling here as well.

[zhangshenhe]

How do I set up static transmitter sampling? I can't find a way to set it up. Thank you.

[Haydnspass]

Hey,
this is not officially supported via the config file, but you can/need to implement it yourself.
Feel free to take a look at the "parse" method of the blinking version https://github.com/TuragaLab/DECODE/blob/master/decode/simulation/emitter_generator.py#L213
and where this is invoked for construction during training.

Best
Lucas