Which algorithms are you trying to test? I’ve been meaning to run some benchmarks using the C.
Let me know if you have any more questions. Note imagesp is my own little script to create a xz projection of the data (I’m often most interested in what is happening in the axial direction). The following script opens the images, preconditions the PSF, and deconvolves using the built in matlab deconvlucy function. I simply import the CElegans image and PSF into imagej (using the import sequence) then save as a single 3D tiff then open in matlab. Hi have been use this excellent matlab tif reader that supports opening 3D and floating point tifs.
I hope the HDF5 code is useful for someone and appreciate any tips or feedback. This dataset has both the stack of the C.elegans data as well as measured PSF stacks. elegans 3D reference data set also from the Biomedical Imaging Group ( ) Does anyone know how to do that in ImageJ or in Matlab? Is this just the central stack where the bead is in sharp focus? Or is it a maximum intensity projection of the stack? I have no idea.Īs reference data (and so we are talking about the same thing) I have been using the C. Secondly, I want to also generate 2D PSFs based on bead imaging (or theoretical PSF using objective and refractive index parameters) as well. Is there another step? Do I need to convert it to an optical transfer function? Am I missing something? I assume now that this 3D Array imported into Matlab is my PSF. (note: there may be an easier way to do this) So far, I have found that I can convert the TIFF to an HDF5 file (.h5) and import that with the following code:
Once I have a 3D TIFF stack, I want to import this into MATLAB. Typically, I have been generating a TIFF stack of 0.1 micron bead, or a theoretical 3D PSFs using the excellent ImageJ plugin by Biomedical Imaging Group in Lausanne ( ). I am familiar with constrained iterative deconvolution and have made 3D TIF stacks of beads before to generate PSFs in programs like Slidebook and Volocity etc. I need the PSFs for testing deblurring algorithms. I am new to coding and image analysis in Matlab and attempting to import theoretical or measured (0.1 micron bead) point-spread-functions (PSFs) in to Matlab.
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