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. This file has been truncated.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. Full field names are used for determining the field name to be used in the NRRD file
% img.metaDataFieldNames: Contains full names of metadata fields that cannot be used as Matlab field names because they contains % special character in their name (such as dot or space). All fields should be listed here that have a % img.metaData: Contains the list of full NRRD field names for each % space_origin: ignored if img.ijkToLpsTransform is defined % space_directions: ignored if img.ijkToLpsTransform is defined % dimension: computed to match dimension of img.pixelData % kinds: computed to match dimension of img.pixelData % type: computed to match type of img.pixelData % sizes: computed to match size of img.pixelData % img.metaData: Contains all the descriptive information in the image header. % coordinate system transformation, the origin of the IJK coordinate system is (1,1,1) to match Matlab matrix indexing % img.ijkToLpsTransform: pixel (IJK) to physical (LPS, assuming 'space' is 'left-posterior-superior') % Write image and metadata to a NRRD file (see )
There is a Matlab writer for NRRD image files here: PerkLab/SlicerMatlabBridge/blob/master/MatlabCommander/commandserver/nrrdwrite.m function nrrdwrite(outputFilename, img) Probably the easiest is to save the reconstructed image as a standard NRRD image file.
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