Presentation by H. Bachimanchi at M2C2, Weizmann Institute, Israel, 5 May 2021

Classification of phytoplankton (blue) and microzooplankton (orange) by holography + deep learning: Schematic of the experimental setup (left). (Image by Harshith Bachimanchi.)
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.

Soft Matter Lab presentations at the SPIE Optics+Photonics Digital Forum

Seven members of the Soft Matter Lab (Saga HelgadottirBenjamin Midtvedt, Aykut Argun, Laura Pérez-GarciaDaniel MidtvedtHarshith BachimanchiEmiliano Gómez) were selected for oral and poster presentations at the SPIE Optics+Photonics Digital Forum, August 24-28, 2020.

The SPIE digital forum is a free, online only event.
The registration for the Digital Forum includes access to all presentations and proceedings.

The Soft Matter Lab contributions are part of the SPIE Nanoscience + Engineering conferences, namely the conference on Emerging Topics in Artificial Intelligence 2020 and the conference on Optical Trapping and Optical Micromanipulation XVII.

The contributions being presented are listed below, including also the presentations co-authored by Giovanni Volpe.

Note: the presentation times are indicated according to PDT (Pacific Daylight Time) (GMT-7)

Emerging Topics in Artificial Intelligence 2020

Saga Helgadottir
Digital video microscopy with deep learning (Invited Paper)
26 August 2020, 10:30 AM
SPIE Link: here.

Aykut Argun
Calibration of force fields using recurrent neural networks
26 August 2020, 8:30 AM
SPIE Link: here.

Laura Pérez-García
Deep-learning enhanced light-sheet microscopy
25 August 2020, 9:10 AM
SPIE Link: here.

Daniel Midtvedt
Holographic characterization of subwavelength particles enhanced by deep learning
24 August 2020, 2:40 PM
SPIE Link: here.

Benjamin Midtvedt
DeepTrack: A comprehensive deep learning framework for digital microscopy
26 August 2020, 11:40 AM
SPIE Link: here.

Gorka Muñoz-Gil
The anomalous diffusion challenge: Single trajectory characterisation as a competition
26 August 2020, 12:00 PM
SPIE Link: here.

Meera Srikrishna
Brain tissue segmentation using U-Nets in cranial CT scans
25 August 2020, 2:00 PM
SPIE Link: here.

Juan S. Sierra
Automated corneal endothelium image segmentation in the presence of cornea guttata via convolutional neural networks
26 August 2020, 11:50 AM
SPIE Link: here.

Harshith Bachimanchi
Digital holographic microscopy driven by deep learning: A study on marine planktons (Poster)
24 August 2020, 5:30 PM
SPIE Link: here.

Emiliano Gómez
BRAPH 2.0: Software for the analysis of brain connectivity with graph theory (Poster)
24 August 2020, 5:30 PM
SPIE Link: here.

Optical Trapping and Optical Micromanipulation XVII

Laura Pérez-García
Reconstructing complex force fields with optical tweezers
24 August 2020, 5:00 PM
SPIE Link: here.

Alejandro V. Arzola
Direct visualization of the spin-orbit angular momentum conversion in optical trapping
25 August 2020, 10:40 AM
SPIE Link: here.

Isaac Lenton
Illuminating the complex behaviour of particles in optical traps with machine learning
26 August 2020, 9:10 AM
SPIE Link: here.

Fatemeh Kalantarifard
Optical trapping of microparticles and yeast cells at ultra-low intensity by intracavity nonlinear feedback forces
24 August 2020, 11:10 AM
SPIE Link: here.

Note: the presentation times are indicated according to PDT (Pacific Daylight Time) (GMT-7)

Harshith Bachimanchi joins the Soft Matter Lab

Harshith Bachimanchi starts his PhD at the Physics Department of the University of Gothenburg on 20th January 2020.

Harshith has a Master degree in physics from the Indian Institute of Science Education and Research, Pune, India, where he submitted a Master thesis in optics, whose results can be found here.

In his PhD, he will focus on microscopy and deep learning.

Seminar on controlled generation of high power optical vortex arrays by Harshith Bachimanchi from IISER Pune, Faraday, 18 September 2019

Controlled generation of high power optical vortex arrays, and their frequency-doubling characteristics
Seminar by Harshith Bachimanchi from the Indian Institute of Science Education and Research, Pune (IISER Pune).

Optical vortices, beams carrying orbital angular momentum (OAM) per photon are of supreme interest in recent times for their wide variety of applications in quantum information, micro-manipulation, and material lithography [1, 2, 3]. Due to a helical phase variation in propagation, and an undefined phase at the centre, these beams have a phase singularity in their wavefront, resulting in the doughnut-shaped intensity distribution. Though the vortex beams have been widely explored in the past, the recent advancements on multiple particle trapping, single-shot material lithography, and multiplexing in quantum information [4] demand an array of optical vortices in a simple experimental scheme.

While the majority of the existing mode converters transform the Gaussian beam into a single vortex beam, the intrinsic advantage of the dynamic phase modulation through holographic technique allow the spatial light modulators (SLMs) to generate vortex arrays directly from a Gaussian beam. However, the low damage threshold of SLMs restricts their usage for high power vortex array applications.

Here, we elaborate a simple experimental scheme to generate high power, ultrafast, higher order optical vortex arrays. Simply by using a dielectric Microlens array (MLA) and a plano-convex lens we generate an array of beams carrying the spatial property of the input beam. Though we’ve verified the technique for the case of optical vortices, it holds true for a useful subset of structured optical beams. Considering the MLA as a 2D sinusoidal phase grating, we have numerically calculated the intensity pattern of the array beams in close agreement with the experimental results. We have also theoretically derived the parameters controlling the intensity pattern, size and the pitch of array and verified experimentally. The single-pass frequency doubling of the vortex array at 1064 nm in a 1.2 mm BiBO crystal produced green vortex arrays of orders as high as lsh = 12, twice the order of the pump array beam, with a conversion efficiency as high as ∼3.65% [5].


  1. Grier, D. G. A revolution in optical manipulation. Nature 424, 810 (2003)
  2. Mair, A., Vaziri, A., Weihs, G. & Zeilinger, A. Entanglement of the orbital angular momentum states of photons. Nature 412, 313 (2001).
  3. Scott, T. F., Kowalski, B. A., Sullivan, A. C., Bowman, C. N. & McLeod, R. R. Two-color single-photon photoinitiation and photoinhibition for subdiffraction photo-lithography. Science 324, 913–917 (2009).
  4. Omatsu, T. et al. Metal microneedle fabrication using twisted light with spin. Opt. Express 18, 17967–17973 (2010).
  5. Harshith, B.S., Samanta, G.K. Controlled generation of array beams of higher order orbital angular momentum and study of their frequency-doubling characteristics. Sci Rep 9, 10916 (2019).

Place: Faraday room, Fysik Origo, Fysik
Time: 18 September, 2019, 15:00