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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
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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
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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
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
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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
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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
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Moiré (2021)
writeup / repo
Angle dependent Ohmic-resistance modelling of twisted-bilayer graphene via sparse linear solvers
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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