A deep learning-enabled portable imaging flow cytometer for cost-effective, high-throughput, and label-free analysis of natural water samples. Academic Article uri icon


  • We report a deep learning-enabled field-portable and cost-effective imaging flow cytometer that automatically captures phase-contrast color images of the contents of a continuously flowing water sample at a throughput of 100mL/h. The device is based on partially coherent lens-free holographic microscopy and acquires the diffraction patterns of flowing micro-objects inside a microfluidic channel. These holographic diffraction patterns are reconstructed in real time using a deep learning-based phase-recovery and image-reconstruction method to produce a color image of each micro-object without the use of external labeling. Motion blur is eliminated by simultaneously illuminating the sample with red, green, and blue light-emitting diodes that are pulsed. Operated by a laptop computer, this portable device measures 15.5cm15cm12.5cm, weighs 1kg, and compared to standard imaging flow cytometers, it provides extreme reductions of cost, size and weight while also providing a high volumetric throughput over a large object size range. We demonstrated the capabilities of this device by measuring ocean samples at the Los Angeles coastline and obtaining images of its micro- and nanoplankton composition. Furthermore, we measured the concentration of a potentially toxic alga (Pseudo-nitzschia) in six public beaches in Los Angeles and achieved good agreement with measurements conducted by the California Department of Public Health. The cost-effectiveness, compactness, and simplicity of this computational platform might lead to the creation of a network of imaging flow cytometers for large-scale and continuous monitoring of the ocean microbiome, including its plankton composition.

published proceedings

  • Light Sci Appl

altmetric score

  • 45.402

author list (cited authors)

  • Grcs, Z., Tamamitsu, M., Bianco, V., Wolf, P., Roy, S., Shindo, K., ... Ozcan, A.

citation count

  • 97

complete list of authors

  • Gӧrӧcs, Zoltán||Tamamitsu, Miu||Bianco, Vittorio||Wolf, Patrick||Roy, Shounak||Shindo, Koyoshi||Yanny, Kyrollos||Wu, Yichen||Koydemir, Hatice Ceylan||Rivenson, Yair||Ozcan, Aydogan

publication date

  • January 2018