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bene51 / SPIM_Reconstruction_Cuda

Fiji plugin wrapping the gpu_deconvolution code
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Weird PSFs #1

Closed tibuch closed 9 years ago

tibuch commented 9 years ago

Hi @bene51

I am working with your Fiji-Plugin. I performed a DoG (sigma = 2, threshold = 0.3) on single channel for the bead based registration and then transformed it with Cuda Transform from your plugin.

Then i extracted the PSFs. psfs

These PSFs produce some line artifacts (with 2-3 iterations) in my deconvolved image.

I also replaced the extracted PSFs with the PSFs from the Preibisch Multiview-Deconvolution (they are more point like). With the Preibisch PSFs I get some better results.

bene51 commented 9 years ago

Hi @tibuch

thanks for reporting. Is there any chance you could share your data?

Extract_PSF_Planes is merely a wrapper around Preibisch's Multiview Deconvolution plugin, to extract the PSFs. So the same results should be obtained. Can you check that the parameters match the ones you use:

https://github.com/bene51/SPIM_Reconstruction_Cuda/blob/master/src/main/java/fastspim/Extract_PSF_Planes.java#L97

Best, Bene

bene51 commented 9 years ago

Just to finish this: PSFs are saved as raw data in 32-bit floating point format in Intel byte order. To open them with Fiji, one needs to choose '32-bit Float' for 'Image type'.