SporeScope combines microfluidics with real-time imaging to enable precise, dynamic monitoring of endospore germination. At its core is a custom-designed PDMS microfluidic chip with compact dimensions optimized for standard microscopy stages. The chip integrates a central hydrogel chamber surrounded by U-shaped support fluidics, allowing nutrient-rich media to flow uniformly around the immobilised bacterial spores.

The structure features:

• Two inlets delivering fresh or mixed media into the support fluidics.

• A single outlet to maintain unidirectional flow and prevent stagnation.

• Selective permeability between the hydrogel and support channels to ensure passive diffusion without spore migration or displacement.

• A printed quadrant system on the chamber to enable repeatable, long-term imaging of fixed regions under the microscope.

The transparent PDMS housing ensures compatibility with:

• Widefield fluorescence microscopy (used in our proof-of-concept)

• Confocal microscopy

• Phase contrast microscopy

This design supports real-time, single-cell imaging of Bacillus subtilis germination. Fluorescent labelling and controlled media input allow researchers to precisely correlate environmental changes with biological responses — something previously not achievable on 2D agar plates or in bulk culture assays.

In future iterations, this system’s compatibility with dual-species cultures, dynamic gradient generation, and a variety of gel formulations (like PEGDA and alginate) further broadens its application in microbiome, clinical, and agricultural studies.