# Pose-Free 3D Quantitative Phase Imaging of Flowing Cellular Populations

arXiv: https://arxiv.org/abs/2509.04848 · HTML: https://mlsanity.com/paper/2509.04848/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 9 of its 41 references that are in the map.
- First posted on arXiv 5 Sep 2025.

## Builds on (most cited first, 9 of 9)

- [DeepSDF: Learning Continuous Signed Distance Functions for Shape Representation](https://mlsanity.com/paper/1901.05103/) (2019)
- [Implicit Neural Representations with Periodic Activation Functions](https://mlsanity.com/paper/2006.09661/) (2020)
- [Occupancy Networks: Learning 3D Reconstruction in Function Space](https://mlsanity.com/paper/1812.03828/) (2018)
- [NeRP: Implicit Neural Representation Learning with Prior Embedding for Sparsely Sampled Image Reconstruction](https://mlsanity.com/paper/2108.10991/) (2021)
- [A Structured Dictionary Perspective on Implicit Neural Representations](https://mlsanity.com/paper/2112.01917/) (2021)
- [Implicit Neural Representation in Medical Imaging: A Comparative Survey](https://mlsanity.com/paper/2307.16142/) (2023)
- [Dynamic CT Reconstruction from Limited Views with Implicit Neural Representations and Parametric Motion Fields](https://mlsanity.com/paper/2104.11745/) (2021)
- [DeepRegularizer: Rapid Resolution Enhancement of Tomographic Imaging using Deep Learning](https://mlsanity.com/paper/2009.13777/) (2020)
- [Missing Cone Artifacts Removal in ODT using Unsupervised Deep Learning in Projection Domain](https://mlsanity.com/paper/2103.09022/) (2021)

## Abstract (arXiv)

High-throughput 3D quantitative phase imaging (QPI) in flow cytometry enables label-free, volumetric characterization of individual cells by reconstructing their refractive index (RI) distributions from multiple viewing angles during flow through microfluidic channels. However, current imaging methods assume that cells undergo uniform, single-axis rotation, which require their poses to be known at each frame. This assumption restricts applicability to near-spherical cells and prevents accurate imaging of irregularly shaped cells with complex rotations. As a result, only a subset of the cellular population can be analyzed, limiting the ability of flow-based assays to perform robust statistical analysis. We introduce OmniFHT, a pose-free 3D RI reconstruction framework that leverages the Fourier diffraction theorem and implicit neural representations (INRs) for high-throughput flow cytometry tomographic imaging. By jointly optimizing each cell's unknown rotational trajectory and volumetric structure under weak scattering assumptions, OmniFHT supports arbitrary cell geometries and multi-axis rotations. Its continuous representation also allows accurate reconstruction from sparsely sampled projections and restricted angular coverage, producing high-fidelity results with as few as 10 views or only 120 degrees of angular range. OmniFHT enables, for the first time, in situ, high-throughput tomographic imaging of entire flowing cell populations, providing a scalable and unbiased solution for label-free morphometric analysis in flow cytometry platforms.