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PreibischLab / BigStitcher

ImgLib2/BDV implementation of Stitching for large datasets
GNU General Public License v2.0
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Deconvolution with BigStitcher #39

Open adamkglaser opened 5 years ago

adamkglaser commented 5 years ago

Hello,

BigStitcher has been amazing for our cleared tissue imaging. I now am interested in exploring the deconvolution capabilities. I was wondering:

  1. Our data is single view (not multi). Is it possible to still use BigStitcher to the deconvolution?
  2. Is it possible to define the PSF from an external file/z-stack? Instead of identifying interest points within the dataset itself.
  3. Are there any extra steps/flags necessary to activate the GPU acceleration?

Thanks! Adam

StephanPreibisch commented 5 years ago

Hi,

  1. yes, that is a standard Lucy-richardson deconvolution then.
  2. yes, in multiview mode, go to PSF, and assign them from file. They need to have odd dimensions with the center of the PSF in the center of the image and the same calibration as the input data
  3. for GPU you need the respective binaries from here: https://github.com/StephanPreibisch/FourierConvolutionCUDALib

Let me know if it works for you! Cheers, Stephan

adamkglaser commented 5 years ago

Ok great, thank you!

Adam