The results per software (website) follow the same enumeration order. The notations ⋅s and ⋅t denote the software and ground truth quantities, respectively. 1. Estimated molecules (): Set of estimated molecules. 2. True molecules (T): Set of true molecules. 3. True Positive (TP): card(S ∩ T). Number of paired molecules. 4. False Positive (FP): card(SS \ S ∩ T). Number of unpaired estimated molecules. 5. False Negative (FN): card(TS \ S ∩ T). Number of unpaired true molecules. 6. Jaccard Index (JAC): TP/(TP + FP + FN). More robust than Recall. 7. Recall: TP/(TP + FN). 8. Precision: TP/(TP + FP). 9. RMSE Volume (RMSE Volum.) [nm]: ${{ }({}\cap {})}}\cap {}} (z^s_i - z^t_i)^2 + (x^s_i - x^t_i)^2 + (y^s_i - y^t_i)^2}$. 10. RMSE Lateral (RMSE Lateral) [nm]: ${{ }({}\cap {})}}\cap {}} (x^s_i - x^t_i)^2 + (y^s_i - y^t_i)^2}$. 11. RMSE Axial (RMSE Axial) [nm]: ${{ }({}\cap {})}}\cap {}} (z^s_i - z^t_i)^2}$. 12. Mean Absolute Deviation volume (MAD Volum.) [nm]: ${{ }({}\cap {})}}\cap {}} |x^s_i - x^t_i | + | y^s_i - y^t_i | + | z^s_i - z^t_i |$. 13. Mean Absolute Deviation lateral (MAD Lateral) [nm]: ${{ }({}\cap {})}}\cap {}} |x^s_i - x^t_i | + | y^s_i - y^t_i |$. 14. Mean Absolute Deviation axial (MAD Axial) [nm]: ${{ }({}\cap {})}}\cap {}} | z^s_i - z^t_i |$. 15. Δx: ${{ }({}\cap {})} }\cap {}} {(x^s_i - x^t_i)}$. 16. Δy: ${{ }({}\cap {})} }\cap {}} {(y^s_i - y^t_i)}$. 17. Δz: ${{ }({}\cap {})} }\cap {}} {(z^s_i - z^t_i)}$. 18. Photons Correlation (Correl. Photons): Pearson correlation $r = }\cap {}} {(p^s_i - )}{(p^t_i - )}}{}\cap {}} {(p^s_i - )^2}} }\cap {}} {(p^t_i - )^2}}}$ with p the photon count and $$ the averaged value. 19. Fourier Shell Correlation (FSC, Volum.) [nm]: Fourier Shell Correlation as defined in  for volume XYZ. 20. Fourier Ring Correlation (FRC yz) [nm]: Fourier Ring Correlation as defined in  for plane YZ. 21. Fourier Ring Correlation (FRC xz) [nm]: Fourier Ring Correlation as defined in  for plane XZ. 22. Fourier Ring Correlation (FRC xy) [nm]: Fourier Ring Correlation as defined in  for (lateral) plane XY. 23. Signal-to-noise ratio volume (SNR Volum.) [dB]: SNR on the volume defined as $20\log\left({I^t - I^s}\right)$ with I the Gaussian rendered image ($\softigma = 5$nm). The volume has 1500 × 1500 × 750 voxels. 24. Signal-to-noise ratio yz (SNR yz) [dB]: SNR on the plane YZ defined as $20\log\left({I^t - I^s}\right)$ with I the Gaussian rendered image ($\softigma = 5$nm). The 2D images I are the results of the projection of all localizations on the plane YZ. 25. Signal-to-noise ratio xz (SNR xz) [dB]: SNR on the plane XZ defined as $20\log\left({I^t - I^s}\right)$ with I the Gaussian rendered image ($\softigma = 5$nm). The 2D images I are the results of the projection of all localizations on the plane XZ. 26. Signal-to-noise ratio xy (SNR xy) [dB]: SNR on the plane XY defined as $20\log\left({I^t - I^s}\right)$ with I the Gaussian rendered image ($\softigma = 5$nm). The 2D images I are the results of the projection of all localizations on the plane XY. Do Moleculewise and cie bouhouh