Tag: Harshith Bachimanchi

Quantitative microplankton tracking by holographic microscopy and deep learning
Harshith Bachimanchi Benjamin Midtvedt, Daniel Midtvedt, Erik Selander, and Giovanni Volpe
Presentation at SPIE-ETAI 2022
San Diego, USA
24 August 2022, 11:45 PDT

The marine microbial food web plays a central role in the global carbon cycle. Our mechanistic understanding of the ocean, however, is biased towards its larger constituents, while rates and biomass fluxes in the microbial food web are mainly inferred from indirect measurements and ensemble averages.Yet, resolution at the level of the individual microplankton is required to advance our understanding of the oceanic food web. Here, we demonstrate that, by combining holographic microscopy with deep learning, we can follow microplanktons through generations, continuously measuring their three dimensional position and dry mass. The deep learning algorithms circumvent the computationally intensive processing of holographic data and allow inline measurements over extended time periods. This permits us to reliably estimate growth rates, both in terms of dry mass increase and cell divisions, as well as to measure trophic interactions between species such as predation events. The individual resolution provides information about selectivity, individual feeding rates and handling times for individual microplanktons. This method is particularly useful to explore the flux of carbon through microzooplankton, the most important and least known group of primary consumers in the global oceans. We exemplify this by detailed descriptions of microzooplankton feeding events, cell divisions, and long term monitoring of single cells from division to division.

Characterising plankton behaviours using deep learning powered inline holography
Harshith Bachimanchi
Presentation at Prof. Ralf Metzler’s Theoretical Physics group at University of Potsdam (Online)
4 February 2022, 14:15 CET

Digital holographic microscopy is a powerful label-free imaging technique for studying biological specimens. The complex optical fields of microscopic objects can be stored in the form of interference patterns and can be reconstructed by using the principles of holography. Recently, we have developed a digital inline holographic microscope with a deep learning powered analysis to track planktons through generations, and continuously measure their three-dimensional position and dry mass. By bringing planktons of different trophic levels together, we were able to perform a quantitative assessment of trophic interactions between planktons such as feeding events, biomass transfer from cell to cell, etc. In this talk, I will be giving a short overview of our method and present some of our recent results.

Microzooplankton classification and their feeding patterns by digital holographic microscopy and deep learning
Harshith Bachimanchi
Presentation at Marine Microbial Chemical Communication (M₂C₂) webinar series
(online) at Weizmann institute of science, Israel
5 May 2021, 15:45 CEST

Phytoplankton and zooplankton are the foundation of the marine food chain. Being an autotrophic primary producer, phytoplankton can generate their own source of energy through photosynthesis. During this process, phytoplankton populations all over the world absorb about 65 Gt (gigatons) of carbon from the atmosphere and thereby equivalently produce the largest amount of oxygen on the earth. The main consumers of this absorbed carbon are the heterotrophic microzooplankton, occupying the next level in the hierarchy of the marine food chain, consuming about two-thirds of the total production (39 Gt). This is likely the largest transition of biological carbon on Earth. Despite being fundamental for our understanding of the carbon cycle and the earth’s climate, the standard estimates leave many questions unanswered at a single microplankton level. Here, we demonstrate that machine learning can be used to estimate the amount of carbon consumed at a single plankton level. We use digital holographic microscopy powered by deep learning to classify planktons by their species and track the biomass of the plankton during individual feeding events. We use the planktonic species, Dunaliella tertiolecta, and Oxyrrhis marina, for our experiments which belong to classes of phytoplankton and microzooplankton respectively. With the help of artificial neural networks, we manage to estimate the carbon consumption and native carbon content at an individual microzooplankton level. Furthermore, we demonstrate the advantages of the approach and compare the results with standard ensemble estimates.