Jason Ken Adhinarta

I am a fourth-year undergraduate at Boston College studying Computer Science and Mathematics. I work as a research assistant at Prof. Donglai Wei’s Computer Vision lab, focusing on the area of connectomics.

I lead the BC Machine Intelligence Group (club Discord), am a member of the BC Experimental Math and Machine Learning Lab, and compete as part of the BC Competitive Programming Team.

Previously, I held a research internship at EPFL’s CVLab where I had the privilege of being mentored by Dr. Jiancheng Yang and Prof. Pascal Fua. Additionally, I interned at Emmerich Research Center under Dr. Eden Steven.

Email  /  CV  /  Google Scholar  /  Github

profile photo
Publications

TriSAM: Tri-Plane SAM for zero-shot cortical blood vessel segmentation in VEM images
Jia Wan, Wanhua Li, Jason K. Adhinarta, Atmadeep Banerjee, Evelina Sjostedt, Jingpeng Wu, Jeff W. Lichtman, Hanspeter Pfister, Donglai Wei
preprint

Frenet-Serret Frame-based Decomposition for Part Segmentation of 3D Curvilinear Structures
Shixuan Gu, Jason K. Adhinarta, Mikhail Bessmeltsev, Jiancheng Yang, Yongjie J. Zhang, Wenjie Yin, Daniel Berger, Jeff W. Lichtman, Hanspeter Pfister, Donglai Wei
preprint

Generating Anatomically Accurate Heart Structures via Neural Implicit Fields
Jiancheng Yang, Ekaterina Sedykh, Jason K. Adhinarta, Hieu Le, Pascal Fua
MICCAI 2024
paper / news

Multiplexed Volumetric CLEM enabled by antibody derivatives provides new insights into the cytology of the mouse cerebellar cortex
Xiaomeng Han, Xiaotang Lu, Peter H. Li, Shuohong Wang, Richard Schalek, Yaron Meirovitch, Zudi Lin, Jason K. Adhinarta, Daniel Berger, Yuelong Wu, Tao Fang, Elif S. Meral, Shadnan Asraf, Hidde Ploegh, Hanspeter Pfister, Donglai Wei, Viren Jain, James S. Trimmer, Jeff W. Lichtman
Nature Communications 2024
paper / news

RibSeg v2: A Large-scale Benchmark for Rib Labeling and Anatomical Centerline Extraction
Liang Jin, Shixuan Gu, Donglai Wei, Jason K. Adhinarta, Kaiming Kuang, Yongjie J. Zhang, Hanspeter Pfister, Bingbing Ni, Jiancheng Yang, Ming Li
TMI 2023
paper / repo

Light storage and thermal-assisted switching of SrAl2O4:Eu2+,Dy3+
Jason K. Adhinarta, Eric Jobiliong, Muhandis Shiddiq, Henri P. Uranus, Eden Steven
JNOPM 2019
paper / poster


Projects

BiomedicalAI4ManufacturingMisc.

GrandChallenge dockerization
SNEMI3D / AxonEM / RNR-EXM

Ported evaluation scripts from connectomics challenges to the GrandChallenge platform

ChunkPipeline
repo

Created a Dask-powered framework for orchestrating data processing pipelines on massive-scale connectomics datasets; ported 3D algorithms (connected components, euclidean distance transform, and TEASAR skeletonization) from the Seung Lab to be chunking-compatible, allowing for efficient utilization of the Boston College Linux Cluster

Mycelium culture contamination detection (2020)
patent application (pending)

Developed and deployed algorithms for fungus contamination detection, used for the automated applicaton of hydrogen peroxide in the development of synthetic leather

Palm oil fresh-fruit-bunch grading (2020)

Standardized grading of palm oil fruit through XGBoost-based classification of color-based features for industrial use

Black soldier fly instance segmentation (2020)

Built an Arduino-based automated data collection system for larvae, used Mask R-CNN and YOLACT++ for instance segmentation; adapted DCNv2 to be compatible with NVIDIA’s APEX for memory-efficient training. Part of a larger project to utilize BSF larvae for waste management

MagicPickle
repo / pypi

magicpickle simplifies the process of transferring pickled representations, making code which both accesses data stored remotely and visualizes it locally easy

SonicSniffer (2023)
repo

A weekend project: attempted to reproduce A Practical Deep Learning-Based Acoustic Side Channel Attack on Keyboards (spectrogram to keystrokes) without hand-crafted feature extraction

SimpleMMO PVP Tool (2021)
site / repo

Developed a web-based tool to allow SimpleMMO players to aggregate results of API endpoint “mining”. Built using a Flask/PostgreSQL/Bootstrap stack

Moiré (2021)
writeup / repo

Angle dependent Ohmic-resistance modelling of twisted-bilayer graphene via sparse linear solvers

Reversing nearness (2020)
writeup / repo

Gradient descent based solution to Al Zimmermann’s discrete optimization contest

Vision-enabled robotic arm (2019)
writeup

Rigged and programmed a 6-DOF arm augmented with (simple) object detection capabilities. Presented at Indonesia Science Expo 2019

Keyboards

I am a huge proponent of split-ortholinear keyboards. I currently run Colemak-DH with Achordion on an Arch. dux


Source adapted from Jon Barron's website