# Photophysical image analysis for sCMOS cameras: Noise modelling and estimation of background parameters in fluorescence-microscopy images

## TL;DR

This paper introduces a new method to estimate background photon levels in fluorescence microscopy images using sCMOS cameras, improving image analysis accuracy.

## Contribution

A novel probabilistic noise modeling approach for sCMOS cameras to estimate the Poisson parameter λbg directly from images.

## Key findings

- The method estimates λbg using a chi-square test and truncated fit technique with strong agreement between sCMOS and EMCCD cameras for low to moderate exposure images.
- The approach incorporates Poisson-distributed photon shot noise and Tukey-Lambda read noise modeling for accurate background estimation.
- Publicly available software enables photophysical image analysis for sCMOS systems.

## Abstract

Fluorescence microscopy is an effective tool for imaging biological samples, yet captured images often contain noises, including photon shot noise and camera read noise. To analyze biological samples accurately, separating background pixels from signal pixels is crucial. This would ideally be guided by the knowledge of a parameter called the Poisson parameter, λbg, representing the mean number of photons collected in a background pixel (for the case when quantum efficiency = 1 and the dark current is negligible).

This study introduces a method for estimating λbg, from an image which contains both background and signal pixels, using probabilistic noise modeling for an sCMOS camera. The approach incorporates Poisson-distributed photon shot noise and sCMOS camera read noise modelled with a Tukey-Lambda distribution. We apply a chi-square test and a truncated fit technique to estimate λbg directly from a general sCMOS image, with camera parameters determined through calibration experiments.

We validate our method by comparing λbg estimates in images captured by sCMOS and EMCCD cameras for the same field of view. Our analysis shows strong agreement for low to moderate exposure images, where estimated values for λbg align well between the sCMOS and EMCCD images. Based on our estimated λbg, we perform image thresholding and segmentation using our previously introduced procedure.

Our publicly available software provides a platform for photophysical image analysis for sCMOS camera systems.