Optimize for maximum likelihood (ML) of the data with the optimized model instead of minimizing the squared deviations. You should use the same distance model for fitting the PSF as you configured in the engine.

This option configures the total number of spots that are used to fit the PSF form. Localizations are scanned and presented until this number of spots is selected.

This option configures the maximum number of spots that are eligible for estimation in each source image. The spots with the highest amplitude are selected, the rest is discarded and not shown in the selection window. If this number is exceeded, the rest of the spots in an image is not displayed. A fractional number can be entered in this field, translating to one spot being picked in each n-th frame. For example, a value of 0.25 selects one spot every fourth frame.

If this option is checked, the selection window (as described above) is shown. Otherwise, all eligible spots are used in estimation.

When fitting multiple layers, fit fluorophore positions in all layers independently. This can mitigate an imprecise plane alignment at the cost of reduced precision.

When fitting multiple layers, fit intensities in all layers independently. This allows fitting a multi-plane data set without knowing the prefactors or making assumptions about fluorophore populations, at the cost of reduced precision and the inability to fit transmission coefficients.

Treat the fluorophore's Z position as ground truth, i.e. do not fit it. This option is useful when calibrating polynomial 3D and in conjunction with setting a ground-truth Z position in the Expression filter output.

Include all pixels into the fit window that are closer than this radius to the selected spot. This is currently an L1 distance.

Assume that the PSF has the same parameters in X and Y, and fit these parameters in common. Enhances estimation precision and stability at the cost of flexibility and thruthful replication of the PSF. This option applies to PSF width and 3D widening factors, but not to the focus plane coordinates, which are controlled by Allow astigmatism

Allow the X and Y focal planes to differ. If this option is unchecked, both planes are set to the same value and fitted together. Checking this option allows fitting data on an astigmatic 3D setup, e.g. with a cylindrical lens.

Assume that the PSF FWHM is the same in all layers, and fit it as a common coordinate. This option is related, but orthogonal to Assume circular PSF.

Assume that the polynomial 3D widening parameters are the same in all layers, and fit them as common coordinates.

When this option is checked, the width of the PSF will be fitted to the data. Otherwise, it will be treated as ground truth and not changed. If the PSF FWHM has been established reliably on other measurements, disabling this option enhances estimation stability and reliability.

When this option is checked, the Z position of the best-focused planes (i.e. the Z positions at which the X and Y PSF FWHMs are smallest, respectively) will be fitted to the data.

When this option is checked, the fluorophore transmission factors are fitted to the data. This allows for straightforward multi-color calibration on live data.