SOPHIA Research Group

HoloBio

HoloBio bridges advanced optics and biology with an intuitive, open-source Python interface for Digital Holographic Microscopy. Perform Real-Time and Offline reconstruction, particle tracking, and quantitative analysis for both DHM and DLHM setups—no programming expertise required.

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HoloBio Interface Screenshot

What it does

DHM Reconstruction

Support for off-axis telecentric, non-telecentric, and other configurations.

DLHM Reconstruction

Methods including Angular Spectrum, KHDI, and Multi-Angle Scanning (MAS).

Flexible Modes

Operate in Real-Time (video-rate) or Offline post-processing modes.

Tools

Tracking, phase profiles, thickness estimation, counting, area quantification, filters, and speckle toolkit.

Installation

pip install holoBio

For more details, check the User Guide.

Video Tutorials

Real-Time DHM Workflow

Select a Topic

Citation

If you use HoloBio in your research, please cite our work:

W. Mona, M. J. Gil-Herrera, E. Mazo, D. Córdoba, S. Obando, M. J. Lopera, R. Restrepo, C. Trujillo, A. Doblas, and R. Castañeda.
"HoloBio: A Holographic Microscopy Tool for Quantitative Biological Analysis"
Under review, PLOS Computational Biology.

Funding

  • The Vicerrectoría de Ciencia, Tecnología e Innovación, Universidad EAFIT.
  • National Science Foundation (Grants 2042563 and 2404769).

Acknowledgment

The authors also express their gratitude to all previous contributors and collaborators whose prior work laid the groundwork for the present work, although they were not directly involved in the development of HoloBio.