SimpleDEMIC

Short Description

Simple non blind deconvolution tool for microscopy using total variation regularization.

Documentation

Description

This plugin is simply the deconvolution part of the EpiDEMIC plugin. It performs Total Variation deconvolution with a known psf.

Principle

The blind deconvolution algorithm EpiDEMIC estimates the PSF and the object that minimizes the following equation:

• The first term of this equation is a likelihood cost function that ensures that the model (object convolved by the PSF) is close to the data. It is a weighted least square criterion.  The pixel dependent weights are given by the precision (the inverse variance) of the noise of each pixel.
• The second term is a regularization function that prevents noise amplification. The regularization function used is an hyperbolic approximation the 3D isotropic total variation (TV). This function favors smooth images with sharp edges. The influence of this regularization function has to be tuned by the mean of the so-called hyper-parameter μ.

Padding

To prevent border artifact the convolution must be performed on a larger size (padding). In theory the padding if the size of the PSF. As this is not always possible in practice, the padding size just has to be reasonably large to prevent artifacts.

Weighting

This step defines the noise model used in the likelihood. The noise is supposed to be Gaussian and independently distributed with a variance that varies across pixels. Therefor, the likelihood must be weighted to give more importance to pixels where the noise variance is lower.

This weight map (i.e. inverse variance map)  can set in different manners:

• uniformly distributed noise of variance = 1,
• computed from either inverse variance or variance maps provided by some calibration steps,
• the noise in microscopy is usually a mixture of photon noise and detector noises. If the mean flux is higher than few photons per pixels, this noise can be well modeled by a non stationary Gaussian noise. In this approximation, the computed variance at pixels k is : where γ is the detector gain (number of photons per quantization level) and  is the variance of the readout noise converted in quantization levels. As before deconvolution the object is not known this computed variance is then approximate by:
• After a first deconvolution at step 3, it is possible to have a better estimate of than data. Furthermore, it is also possible to perform a linear regression to automatically estimate detector gain and readout noise.

Some pixels can be dead or saturated. This will destroy the linearity assumed in the convolution model. These pixels must be flagged by zeros in the binary bad data map.

Deconvolution

Once the data and the noise model are set, it is preferable to perform deconvolution with the aberration free PSF before running the full blind deconvolution algorithm. In this step, it will be possible to tune the regularization level (hyper-parameter μ) and to ensure that no artifact (such as border artifact due to a too narrow padding) will appear.

The main parameters of this panel are  the regularization function parameters that is (for an object f):where:

• μ is the regularization level (hyper-parameter). It ensures the balance between likelihood and regularization. If it is too small the result will be very noisy. If it is too large, details will be smoothed out and the result will be patchy. As it depends of the spatial structure of the objet and the noise level, there is no simple way to choose it and it has to be set by trials and errors. Its behavior is logarithmic and it is more convenient the tune the logarithm of the regularization level
• is the finite difference of the object f at pixel k and along dimension i,
• are the aspect ratio of a voxel.It should be automatically set according to the pixel size.
• ε is a threshold used to smooth the total variation function. The smaller it is the closer to the pristine total variation is the regularization. To help to remove spurious noise this threshold should be similar to the effective quantization level (automatically set as the maximum of the data / 1000).
• By default the object is assumed to be non-negative,

The deconvolution algorithm is iterative. As a consequence, the solution depends on:

• the number of iteration that has to be such has the deconvolved object does not vary from an iteration to another,
• the initial image given as a starting point.

Tips

• To perform deconvolution, the data must be correctly sampled according to the Nyquist criterion. This can be checked by carefully examinating the PSF.
• Due to java limitation, the padded output cannot be larger than 2^31 pixels.
• The memory footprint of the plugin i can be halved by computing in single precision.
• Pixels with values equal to the data type highest value are automatically considered as saturation.
• The regularization level have to be manually tuned. However it should remain constant for all images coming from the same experiments. All the parameters  for a dataset can be saved and conveniently loaded to be used for another dataset.

DEMICS on server

Deconvolution is a memory and computation intensive task and it may not fit in end-users laptop. To process batches of large datasets, both plugins can be used without the Icy GUI on any server with Docker.

See also the EpiDEMIC plugin.