just doing my duty (cycle)

hello!

this is plugin for fiji. it's a very basic fluorophore photophysics simulator that will get you a blinking dataset. the photophysical properties are based on table 1 in dempsey et al (2011).

how to use it

you can supply a ground truth image to the plugin, or else it will just use an inbuilt test structure (a ring of diameter 1000nm with 50 fluorescent molecules evenly distributed around the circumference). there's an example ground truth on my repo called 'GT.tif'. it's a unicorn. of course.
if you supply your own ground truth this will need to be a binary image - the plugin takes every pixel with a value above zero as being a particle to simulate. use big ground truth images containing lots of non-zero pixels at your peril.
select the fluorophore and buffer that you wish to simulate, and supply the length of time for the 'experiment', exposure time, and ground truth pixel size. again, simulate long experiments at your peril (it handles e.g. 5 minute experiments fine, but i'm afraid to see how far i can push it).

what it does

• generates trajectories for each molecule in the image with calculated on/off times, photon yields and survival fractions.
• adds poisson noise. no background
• renders molecules with a gaussian psf of size determined by the fluorophore wavelength (it assumes a 1.4 na objective)
• assumes quantum efficiency of 1 photon -> 1 electron
• multiplies by em gain of 100
• downsizes image to a camera chip with 100nm pixels
• adds gaussian read noise with standard deviation = 50
• adds baseline count of 100 to each camera pixel
• multiplies by em factor for sqrt(2).

this workflow is based loosely on that from sage et al (2015) - hit me up if i've done something in the wrong order.

output

you'll get an image stack out where the first frame is the widefield equivalent with all molecules 'on', and then the rest of the stack is blinking fluorophores. should be happily analysable with your favourite super-resolution reconstruction algorithm after that.

disclaimer

obviously this code is not peer-reviewed, but people have shown interest in this as a useful tool. also, i have not optimised the code at all so it might be slow or break your computer. i accept no responsibility for this, but sorry if that happens.

let me know if you have any questions!

cuddles,
siân x

GPU-independent error mapping

Test release for users whose graphics cards object to NanoJ libraries.
UPDATED 10/06/2020 to include documentation pdf

morsey christmas

excellent tool for procrastination, low-key trolling of coworkers and subliminal messaging.
put the .jar file in your fiji plugins folder.
you're welcome.