Hi, I'm Sanket, a PhD researcher specializing in high-precision optomechanics and super-resolution microscopy at the Italian Institute of Technology and University of Genoa. My research focuses on developing cutting-edge single-molecule localization microscopy systems achieving sub-10 nm precision and ultra-stable sample positioning with sub-nanometer accuracy.
I'm passionate about building custom optical instruments that push the boundaries of what's measurable at the nanoscale. My work combines expertise in nanosecond pulsed laser systems, high-precision optomechanical alignment, real-time signal processing, and GPU-accelerated algorithm development to create tools that enable scientists to observe biological processes at unprecedented resolution.
Beyond the lab: I maintain a strong interest in cybersecurity and threat intelligence, developing Python-based tools for security analysis in my free time. I also enjoy competitive squash (former Institute Team Captain), following football across the world, and staying current with the latest developments in both microscopy and cyber threat landscapes.
Research
PhD Work & Projects in High-Precision Optomechanics
ISM-FLUX: Custom MINFLUX with SPAD Array Detector
2023 - Present | Molecular Microscopy and Spectroscopy, IIT, Italy
Developed a custom MINFLUX-like single-molecule localization microscope with a 5×5 SPAD array detector achieving single-digit nanometer localization precision. Key achievements include:
Designed and calibrated orbital excitation scanning patterns achieving <10 nm localization precision for single-molecule detection
Implemented GPU-accelerated maximum-likelihood localization algorithms using molecule detection functions (MDFs), improving computation speed by up to 105×
Extended localization range by ~36× to 600×600 nm2 with unbiased localization for emitters both inside and outside the targeted coordinate pattern (TCP)
Expanded ISM-FLUX functionality by integrating custom-built STORM module for widefield super-resolution imaging
Designed and built a modular 3D active stabilization add-on for custom microscopes achieving sub-nanometer sample stabilization (<1 nm drift correction in all three axes).
Developed real-time feedback control system with <1 nm positioning accuracy in X, Y, and Z axes
Created open-source hardware and software solution compatible with existing microscope platforms
Implemented high-bandwidth piezo-based correction achieving millisecond response times
Active StabilizationSub-nanometer PrecisionOpen-Source HardwareReal-time ControlPiezo Systems
Open-Source Hardware and Software 3D Active Stabilization for Super-Resolution Microscope
Focus on Microscopy 2024 | Genoa, Italy
Poster
Open-Source Hardware and Software Active Stabilization for Super-Resolution Microscopy
Single Molecule Localization Microscopy Symposium 2023 | Vienna, Austria
Poster
Automating Superresolution Microscopy Image Analysis with a Novel Deep Learning Architecture to probe Intracellular Trafficking
66th Biophysical Society Annual Meeting 2022 | San Francisco, USA
Teaching Experience
Sharing Knowledge in Optical Engineering
Optical Engineering Instructor
Nikon School | Italian Institute of Technology & NIC@IIT, Genoa
2023, 2024
Delivered hands-on training in optical engineering principles and microscopy techniques to researchers and students. Covered topics including optical alignment, fluorescence microscopy, and super-resolution imaging fundamentals.
Assisted in laboratory sessions and tutorials for graduate-level optical microscopy course. Guided students through practical experiments in fluorescence imaging and image analysis techniques.
Side Projects
Cybersecurity & Python Tools
Personal projects developed during my PhD exploring cybersecurity and threat intelligence.
Comprehensive step-by-step guide on setting up your personal MISP instance on a cloud compute machine. Covers everything from server provisioning to enabling threat intelligence feeds.
Successfully qualified The National Abacus & Mental Arithmetic and Mathematics Test conducted by International Abacus Mathematics Association
Research Scholarship
Proud recipient of SAGNIK ASIS RAY SCHOLARSHIP for biological research
Mental Math
Qualified Advance Level Of Mental Math Arithmetic Course
Sports & Leadership
Squash Ranking
Ranked 34th (out of 6600+ players) in All India Men's Squash Ranking by Squash Racket Federation of India (SRFI)
Inter-IIT Sports Meet
Captained the team to the Silver Medal in the Squash Championship during the Inter-IIT Sports Meet 2019
Tournament Victories
Led the team to Victory in Squash Championship, in Spardha' 2018, and Udghosh' 2019
State Level Achievements
Achieved 3rd place in Uttar Pradesh squash opens and 5th place in Maharashtra state squash opens
Sports Scholarship
Proud recipient of Sports scholarship by Indian Institute of Technology, Kanpur for outstanding performance in Squash
Short Bio
Where am I in my journey?
Be Part Of the Story!
Future with you?
I'm keeping an open mind about where my future takes me, but
if you think I would be a great fit for your team, company or project, let me
know! I'd love the chance to talk with you. Feel free to also send cat
pictures, I always appreciate those. For opportunities and cat related
enquiries, there's a button right below.
2022 to Beyond!
As PhD goes
To nurture my passion for building awesome super-resolution microscopes that can revolutionize science, I decided to start my PhD in Optophysics and Engineering. This feels like one of the best decisions that I have made in my life.
Here we do awesome science and we are extremely motivated to solve any challenge that comes our way. A further plus point is that everybody in the group is friendly and it feels like a family to work with.
2021-2022
Mastering 'Things'
Afterwards, I was amazed by the power of deep learning so much that I decided to undertake a Masters degree in this field at IIT Kanpur. My aim was to bring a more logical approach to the image processing pipeline of biological imaging data such that it can be more accessible to common folk without needing black magic-like skills.
During my time at IIT, I was fortunate to build a custom super-resolution microscope from scratch. An experience that changed my perspective towards what I want to do for my PhD.
2017-2021
Engineer!
I was accepted by the Indian Institute of Technology, Kanpur, following high school and moved there in August 2017 to embark on the next stage of my journey - a Bachelor's degree in Biological Sciences and Bio-Engineering.
I felt like a deity; combining the knowledge of electronics with cell biology was like exploring the universe at a pixel level. I was fortunate enough to be able to use different microscopes and see life at a nano level. Then deep learning gave me the power to make computers work without me working, and now the sky is the only limit.
2005-2017
The Story Begins
I was a student at Kendriya Vidyalaya in Maharashtra,
India; progressing to join the Higher Secondary Education (HSE) programme. All
of the IB subjects I took, except languages and literature, were taught in
English. My high-level elective classes were Maths, Physics and Chemistry. I selected
Electronic engineering as my elective during the +2 degree.
Analyzing and monitoring DNS data of a domain is a challenging task. DNS data is complex and requires a deep understanding of DNS protocols and the latest security threats. DNS protocol has so many facets that it becomes hard to remember what has been configured and what is missing. At times, people tend to forget to configure or update the DNS records, which can lead to security threats such as DNS hijacking, subdomain takeover, Email Spoofing/Interception, etc. So I decided to build a tool that can analyze the DNS data of a domain and provide a report with the latest security threats and recommendations to fix them.
This tool is developed in Python using Streamlit and is hosted on Google Cloud Platform. It is a user-friendly web-based tool that can be used by anyone without the need to understand or learn Python to analyze the DNS data of a domain. It is designed to provide as detailed information regarding various types of DNS records and their current configurations for a given domain. I planned it in such a way that it can be used by both blue and red team security professionals.
I like to understand and play with DNS resolvers and the protocol, so this was a fun project to work on for me. This was the first time I used Google Cloud Platform to host my web application directly. Although the website is hosted on the free tier of Google App Engine, it is still a great experience for any user to use it. I also learned a lot in depth about the DNS protocol and the latest security threat landscape using DNS. Overall, it was a great experience to work on this project and hope people find it useful.
ThreatHarvester - IOC Aggregator
Cyber Threat Intelligence, Python, IOC enrichment, API Integration
Demo of ThreatHarvester tool showing IOC enrichment and aggregation using local DB check and API calls
I am relatively new to the field of cyber security and threat intelligence. I like the field of cyber threat intelligence and I found out about it during one of the SANS training courses and Flare trainings. Since then I am continuously learning and understanding the basics of threat intelligence. I find it very fascinating and I like to play with IOCs and indicators of compromise. While I was learning about threat intelligence and fiddling with IOCs, I understood that there are many resources for getting the IOCs. However it is very tedious to analyze one by one on each website and resource. So I thought of building a tool for searching and aggregating the IOCs from various resources and websites using a single command line interface.
It is a CLI tool completely written in Python. It uses a local DB to store the IOCs and a set of APIs to get the IOCs from various resources and websites. The tool accepts IOCs as input and returns the aggregated results from various resources and websites. IOC can be a domain, IP, MD5, SHA1, SHA256, etc. It also allows the user to turn on/off the sources and resources to get the IOCs from for more granular control. However this project does require at least starting knowledge of Python.
This project started out of sheer interest in the field of cyber threat intelligence and now has become somewhat of a passion for me. I am working on it during my free time and will be adding more features to it in the future. I hope it will be useful for others as it is useful for me.
Web-hosted Personal MISP Instance
Threat Intelligence, MISP, Malware Analysis, Web hosting
Well this one was a fun project. It started as one of the resources that I needed for the ThreatHarvester project. But then I quickly realized that MISP registrations are blocked and the only way forward was to make my own server. I almost gave up on the idea, but then I found out that I can host my own MISP instance on a cloud server.
After looking around I found out about Hetzner and their affordable cloud servers (for a student like me). So I decided to go for Hetzner Compute server and host my MISP instance on it. I started looking into the documentation and requirements for hosting the MISP instance and found out that I would need somewhat of a knowledge Apache web server. So with the help of the official documentation and some google searches, trial and error, some AI help (mostly for Apache configs), and a lot of head-banging, I was able to host my MISP instance on the cloud server.
For fun I also configured a custom domain using Cloudflare for my MISP instance. I also configured a custom SSL/TLS certificate for HTTPS of my domain using Let's Encrypt. And finally for the feeds, I selected the ones that are most relevant to me and my interest in Cyber Threat Intelligence. It was a fun experience through which I was able to learn a lot about the MISP and the threat intelligence field. I am also planning to integrate this into the ThreatHarvester project and make it a more useful tool for the community.
