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losonczylab / sima

Python package for analysis of dynamic fluorescence microscopy data
GNU General Public License v2.0
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Optionally apply Gaussian blur & Laplacian before dftreg #250

Closed neurodroid closed 5 years ago

neurodroid commented 5 years ago

Following a suggestion by Olivier Dupont-Therrien (Doric Lenses Inc), optionally apply a sequence of Gaussian & Laplacian filter before performing motion correction with dftreg. This strategy can eliminate static inhomogeneities such as vignetting from the images, and is particularly useful for 1-photon widefield microendoscope data acquired through a GRIN lens. Example data: Raw images without correction: https://www.dropbox.com/s/pericx3h1jqzppm/20180919_BG0039_sensor0_0000_corr.tif?dl=0 Images with standard dftreg: https://www.dropbox.com/s/bzl79wofuwy8fzi/20180919_BG0039_sensor0_0000_corr_sima_mc_lp0_final.tiff?dl=0 Images with laplace filter (sigma=8) followed by dftreg: https://www.dropbox.com/s/r6ng6ycxoxkzfhl/20180919_BG0039_sensor0_0000_corr_sima_mc_lp8_final.tiff?dl=0

Dropbox pw: laplace

jzaremba commented 5 years ago

Great, thanks.

It looks like this also includes a fix for #242 that @james-priestley may have fixed elsewhere. I don't see a reason to not include this as well here, so I'll merge it in.