Summary of the ISBI 2013 Grand Challenge on 3D Deconvolution Microscopy

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1 Summary of the ISBI 23 Grand Challenge on 3D Deconvolution Microscopy Cédric Vonesch & Stamatios Lefkimmiatis Biomedical Imaging Group EPFL, Lausanne, Switzerland April 7, 23

2 Thanks to our sponsors! ISBI 23 Grand Challenge Organizers: Stephen Aylward Bram van Ginneken Bio Imaging & Signal Processing Technical Committee IEEE Signal Processing Society Financial support for awards! Funding: 2

3 About the organizers Main organizers: Expert committee members: Cédric Vonesch EPFL Lausanne, Switzerland Stamatios Lefkimmiatis EPFL Lausanne, Switzerland Laure Blanc-Féraud CNRS Sophia Antipolis, France Rainer Heintzmann Friedrich-Schiller-Universität Jena, Germany Arne Seitz EPFL Lausanne, Switzerland Michael Unser EPFL Lausanne, Switzerland 3

4 Primary goal: promoting cross-fertilization GFP Biology & Medicine Independent/ communitysupported developers Commercial software providers CCD Optics & Photonics Academic algorithm designers FFT Signal Processing & Applied Math 4

5 Overview of the challenge Months 3 ISBI special session Final Invite participants with best results to present their method 2 Qualification Determine the performance of proposed methods Larger data, less oracle information Training Familiarize participants with data sets, forward model, metrics... Simplified setting

6 Typology of the phantom data Manifold Structural Mathematical Corresponding Stain Color dimension class representation biological objects example channel (nm) Point sources, sub- Dirac distributions, Single molecules, MitoTracker Yellow/ 6 resolution structures narrow B-splines vesicles, mitochondria Orange Curves Bézier polynomials Microtubules, actin GFP Green 525 filaments 2 Surfaces Deformable Cellular or nuclear DiD Deep 675 ellipsoidal contours membranes Red 3 Dense volumes Wide B-splines Condensing DAPI, Blue 45 chromatine, DNA Hoechst 6

7 Summary of the forward model y = Q P(Tx + b)+n (, 2 I) Notations: x: ground-truth fluorophore distribution T: block-toeplitz matrix b: background signal (constant vector) 2 : variance of Gaussian noise Q: quantization and clipping operator Q(x) = 8 < arg min n2n x n if x>, : otherwise 7

8 Simulated micrographs (Maximum-intensity projections) 8

9 Simulated micrographs (Maximum-intensity projections) 9

10 Performance Metrics MSE-based Metrics Increase in signal-to-noise ratio (ISNR) ky xk ISNR = 2 log 2 x kˆx xk 2 : ground-truth ˆx : affine regressed reconstruction Normalized mean integrated squared error (NMISE) NMISE = N NX n= [T (x ˆx)] 2 n [Tx] n Structure Similarity Index (SSIM) Better correlation with human eye perception than SNR Mean-SSIM, Minimum-SSIM (over all slices of the 3D volume) Wavelet sparsity index Measure of the number of nonzero coefficients in the wavelet domain

11 Performance Metrics Derivative-based metrics Relative total variation error R = P N n= k[rˆx] n [rx] n k 2 P N n= k[rx] n k 2 Relative structure-tensor error P N n= R = k[sˆx] n k k[sx] n P k N n= k[sx] n k Relative Hessian-Frobenius error Sx = G rx rx T 3X q k[sx] n k = [ k] n k= R = P N n= k[hˆx] n k F k[hx] n k F P N n= k[hx] n k F k[hx] n k F = q [ ] 2 n +[ 2] 2 n +[ 3] 2 n

12 Performance Metrics Fourier-based metrics Fourier shell correlation: measures the normalized cross-correlation coefficient between two 3D volumes over corresponding shells in Fourier space FSC (!) = P! i 2! ˆX (! i ) X (! i ) q P!i2! ˆX (! i ) 2 P! i 2 X (! i) 2 Relative energy regain G R (!) = P! i 2! ˆX (! i ) X (! i ) 2 P! i 2! X (! i) 2 G R (!) = G R (!) = : spatially frequency domain perfectly reconstructed : no available frequency information 2

13 Results (top submissions)

14 Results (top submissions)

15 Results (top submissions)

16 Results (top submissions)

17 Results (top submissions)

18 Results (top submissions)

19 Summary of the challenge X Measured This year s awardees (SPS-sponsored prizes): Y. Ferréol Soulez, Lyon University ($5) 2. David Biggs, KB Imaging Solutions ($3) 3. Hiep Luong, Gent University ($2) Next edition: Deconvolved Online submission system to reopen soon Take up the challenge & submit your result! Best entries will win ISBI 24 travel grants! Visit our website for updates: 24 bigwww.epfl.ch/deconvolution/challenge X Z Measured Deconvolved 9