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bioRxiv · 10.64898/2026.10.21.760683

A method for correcting background non-uniformity while preserving specimen-level information in Fourier ptychographic microscopy images

Copeland, L.·Polland, K. F. E.·Walker, L.·Amos, W. B.·Baxter, K. J.·Shaw, M. J.·McConnell, G.
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Abstract

Fourier ptychographic microscopy (FPM) enables high resolution imaging across large fields of view, but reconstructed images often exhibit background non-uniformity that interferes with quantitative image analysis. Here, a post-reconstruction background correction approach is presented that identifies specimen-containing regions and corrects only the surrounding background, leaving specimen pixel intensities unchanged. The method was effective across amplitude and phase reconstructions of multiple biological specimen types with no loss in image resolution. The method also improved object detection compared with analysis of the uncorrected image data. FPM background correction reduced residual background non-uniformity to 0.61% with only 0.04% structural error, compared with 6.13% structural error for pseudo flat field correction. These results demonstrate that FPM background correction can support more accurate quantitative analysis of FPM image data while preserving specimen information and image resolution, enabling more reliable segmentation and measurement across large fields of view.

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Copeland, L., Polland, K. F. E., Walker, L., Amos, W. B., Baxter, K. J., Shaw, M. J., McConnell, G.. 2026-10-23. A method for correcting background non-uniformity while preserving specimen-level information in Fourier ptychographic microscopy images. https://doi.org/10.64898/2026.10.21.760683

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