Extended Depth of Field

(Left) With EDF. (Right) Without EDF

Extended depth of field algorithm is a proven method of generating a best focus composite image from a z-stack. The particular complex wavelet implementation used in CODEX is Saphicon AllFocus, following the technique first described by Brigette Forster in 2004. This allows for the best image quality and advantages of smaller processed datasets without losing meaningful fluorescence data. This algorithm can be toggled off for backwards compatibility with 3D volumetric output.

Forster, B., Van De Ville, D., Berent, J., Sage, D., & Unser, M. (2004). Complex wavelets for extended depth‐of‐field: A new method for the fusion of multichannel microscopy images. Microscopy research and technique, 65(1‐2), 33-42.

ImageJ Implementation