Estimating full-field displacement in biological images using deep learning

Solomon Warsop, Soraya Caixeiro , Marcus Bischoff, Jochen Kursawe, Graham David Bruce, Philip Wijesinghe*

*Corresponding author for this work

Research output: Working paperPreprint


The estimation of full-field displacement between biological image frames or in videos is important for quantitative analyses of motion, dynamics and biophysics. However, the often weak signals, poor biological contrast and many noise processes typical to microscopy make this a formidable challenge for many contemporary methods. Here, we present a deep-learning method, termed Displacement Estimation FOR Microscopy (DEFORM-Net), that outperforms traditional digital image correlation and optical flow methods, as well as recent learned approaches, offering simultaneous high accuracy, spatial sampling and speed. DEFORM-Net is experimentally unsupervised, relying on displacement simulation based on a random fractal Perlin-noise process and optimised training loss functions, without the need for experimental ground truth. We demonstrate its performance on real biological videos of beating neonatal mouse cardiomyocytes and pulsed contractions in Drosophila pupae, and in various microscopy modalities. We provide DEFORM-Net as open source, including inference in the ImageJ/FIJI platform, for rapid evaluation, which will empower new quantitative applications in biology and medicine.
Original languageEnglish
Publication statusPublished - 24 May 2024


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