Deconvolution is one of the most common image-reconstruction tasks that arise in 3D fluorescence microscopy. The aim of this challenge is to benchmark existing deconvolution algorithms and to stimulate the community to look for novel, global and practical approaches to this problem.

The challenge will be divided into two stages: a training phase and a competition (testing) phase. It will primarily be based on realistic-looking synthetic data sets representing various sub-cellular structures. In addition it will rely on a number of common and advanced performance metrics to objectively assess the quality of the results.

`psnr.m`

script.

- \(x\) : Reconstructed image stack (3D MATLAB array).
- \(f\) : Ground-truth image stack (3D MATLAB array).

- \(p\) : Peak value used in the computation of PSNR (Default: maximum value of \(f\)).

- \(\textrm{psnr}\) : Peak signal to noise ratio.
- \(\textrm{mse}\) : Minimum mean squared error between \(x\) and \(f\).

`nmisec.m`

script.

- \(x\) : Reconstructed image stack (3D MATLAB array).
- \(f\) : Ground-truth image stack (3D MATLAB array).
- \(f_b\) : Intermediate result, \(f_b=\mathbf{A}\mathbf{x}+\mathbf{b}\), of the observation model (3D MATLAB array). Output of the
`ForwardModel3D.m`

script.

- \(\textrm{nmise}\) : Normalized mean integrated squared error between \(x\) and \(f\).

`ssim3D.m`

script which can be applied to image volumes.

- \(x\) : Reconstructed image stack (3D MATLAB array).
- \(f\) : Ground-truth image stack (3D MATLAB array).

- \(K\) : constants in the SSIM index formula (see ssim_index.m) (Default : \(K\) = [0.01 0.03]).
- \(\textrm{window}\) : local window for statistics (see ssim_index.m). The default window is Gaussian given by
`window = fspecial('gaussian', 11, 1.5)`

. - L : dynamic range of the images (Default: maximum value of \(f\)).

- \(E\) : The mean ssim index over all the slices of the image stacks.
- \(M\) : The minimum ssim index over all the slices of the image stacks.

`FourierShellCorrelation.m`

script.

- m : Output of the
`FourierMetricsConstructor.m`

script. - \(\hat{f}_1\) : The Fourier transform of the reconstructed image stack.
- \(\hat{f}_2\) : The Fourier transform of the ground-truth image stack.

- \(\mbox{FSC}\) : The Fourier shell correlation as defined above.

`RelativeEnergyRegain.m`

script.

- m : Output of the
`FourierMetricsConstructor.m`

script. - \(\tilde{I}\) : The Fourier transform of the reconstructed image stack.
- \(\tilde{O}\) : The Fourier transform of the ground-truth image stack.

- \(\mbox{G}_R\) : The relative energy regain.

The registered participants will receive soon a personalized upload link.

January 6, 2014The evaluation stage of the second edition of the challenge has started.

November 6, 2013The official stage of the challenge will last around 2 months.

November/December, 2013The training stage of the second edition of the challenge has started. Follow this link to register and receive e-mail updates.

July 17, 2013