SergeDmi
commented
2 years ago Dear Jakob,
Thanks for your interest in cGN :)
The file is actually in the repo : https://github.com/SergeDmi/ConfocalGN/blob/master/gauss_psf.tiff In the default example, the psf is a 3D gaussian of variance 13.0, 13.0, 22.0 -- but a filename for a 3D image can be provided as well. gauss_psf.tiff is thus a 3D stack.
As far as I know, PSF from PSF generator should directly work - but tiff images can be tricky sometimes so I would recomend to do a unit test before (e.g. convolve it with a very simple ground truth image such as a single dot).
Cf confocal_generator.m : https://github.com/SergeDmi/ConfocalGN/blob/master/cgn/confocal_generator.m
% * conf.psf is the point spread function of the microscope
% it is the 2-way psf (i.e. illumination+observation)
% also called confocal psf
% It can be :
% - Either a 1x3 vector
% this assumes the psf to be gaussian (which provides fast convolution)
% the PSF is in units of the size of original image pixel
% ex : psf = [wx,wy,wz] where wi is the gaussian spread on axis i
% - or an image to be convolved to the ground truth image
% In this case, make sure the grount truth image and the PSF image have
% pixels of the same physical size
jabruniessner
Dear Dr Dmitrieff,
I am sorry to disturb you.
in the search of a good tool for generating realistic confocal images, I stumbled across yours and Dr. Nedelecs program ConfocalGN. I managed to get to run the example, however in the paper it says that the example runs setting the parameter
conf.psf = "gauss_psf .tiff ",
but in the example file cgn_example.m on github the paramter is set to
conf.psf=[13 13 22];
Moreover, I could not find the file gauss_psf.tiff on the github repository. I am curious for the file because I would like to use it after generating a PSF function in form of a tifffile. I used the FIji plugin PSF Generator, which returns a stack of images instead if a single 2D image. Does the program also work with that?
Thank you for your time and best regards
Jakob Niessner