Destriping of Light Sheet data

We’ve been working on a simple, home-built light sheet system in the NIC. It’s designed for imaging cleared organs, and so uses a cylindrical lens to produce a light sheet, about the simplest illumination system you can use for such a microscope (it’s similar to the system described in [1]). Because the illumination traverses the sample, if there is an opaque or scattering part of the sample, it blocks part of the illumination beam, casting shadows through the sample that show up as stripes in the resulting images.

I recently discovered a software tool for removing stripes from these images [2]. It’s not perfect – in particular, it assumes that the noise is additive, when it is really multiplicative – but it does a good job. You can download a Fiji plugin that implements it here, and you can see the results below.

Raw image

Raw image

After destriping

After destriping

References

  1. H. Dodt, U. Leischner, A. Schierloh, N. Jährling, C.P. Mauch, K. Deininger, J.M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, "Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain", Nature Methods, vol. 4, pp. 331-336, 2007. http://dx.doi.org/10.1038/nmeth1036
  2. J. Fehrenbach, P. Weiss, and C. Lorenzo, "Variational Algorithms to Remove Stationary Noise: Applications to Microscopy Imaging", IEEE Transactions on Image Processing, vol. 21, pp. 4420-4430, 2012. http://dx.doi.org/10.1109/TIP.2012.2206037

One thought on “Destriping of Light Sheet data

  1. I had some very helpful discussions with Pierre Weiss where he showed me how to destripe log-transformed data as an approximation to the multiplicative case. This works even better than the example shown above.

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