Portrait of Amirhossein Kardoost

Amirhossein Kardoost

amirhossein.kardoost [at] helmholtz-munich.de

I am a machine learning and computer vision engineer based in Munich, currently at Helmholtz Munich (Institute of AI for Health). I build AI systems for complex visual data at scale, from natural images and videos to 2D and 3D microscopy, and I ship them as tools.

I focus on machine learning and computer vision problems like segmentation, tracking, multimodal learning, and self-supervised learning. Alongside the models, I build the machine learning infrastructure that turns these methods into reliable systems on real imaging data. I work end-to-end, from data annotation, model training and distributed GPU workflows to deployable tools, interactive GUIs, and data management platforms.

Previously, I was a software engineer at European XFEL, where I built computer vision pipelines, databases, microscopy data management systems, hardware control interfaces, and web tools for experimental workflows at scale.

I received my Ph.D. in Computer Science, magna cum laude, from the University of Siegen, where I worked on video instance and motion segmentation under the supervision of Prof. Margret Keuper. Prior to that, I completed my Master's in Computer Science from Saarland University.

Softwares

macrophage-napari

Macrophage-Napari

A Napari based GUI for 2D detection, 3D segmentation, and 2D/3D annotation of macrophages in volumetric microscopy data.

neurogenesis-napari

Neurogenesis-Napari

A Napari based GUI for cell detection and classification in multi channel fluorescent images.

Datasets

Crystals Dataset

Crystals Dataset

Brightfield microscopy images and manually annotated pixel level masks for crystal instances of small, star, and rectangular shapes.

3D Macrophage Dataset

3D Macrophages Dataset

Multi channel fluorescent z-stack images and corresponding 3D pixel-level segmentation masks for macrophage instances.

Selected Publications

HASSL

HASSL: Hierarchy-Aware Self-Supervised Learning Framework for Single Cell Microscopy

Julius Riel*, Vishwa Mohan Singh*, Sai Anirudh Aryasomayajula, Anuun Chinbat, Hannes Leonhard, Moritz Ladenburger, Frederik Alexander, Vishisht Choudhary, Fabio Laredo, Giacomo Masserdotti, Thorben Prein, Carsten Marr†, Amirhossein Kardoost(* equal contribution, † corresponding author)

ECCV, 2026

3D Masked Autoencoders

3D Masked Autoencoders are Robust Learners of Volumetric and Multimodal Cellular Representations for Microscopy

Amirhossein Kardoost, Lion Gleiter, Tingying Peng, Carsten Marr

arXiv, 2026

Convolutional Neural Network Approach

Convolutional Neural Network Approach for the Automated Identification of in Cellulo Crystals

Amirhossein Kardoost, Robert Schönherr, Carsten Deiter, Lars Redecke, Kristina Lorenzen, Joachim Schulz, Iñaki de Diego

Journal of Applied Crystallography, 2024

Higher-Order Multicuts

Higher-Order Multicuts for Geometric Model Fitting and Motion Segmentation

Evgeny Levinkov*, Amirhossein Kardoost*, Bjoern Andres, Margret Keuper (* equal contribution)

TPAMI, 2022

Uncertainty in Minimum Cost Multicuts

Uncertainty in Minimum Cost Multicuts for Image and Motion Segmentation

Amirhossein Kardoost, Margret Keuper

UAI, 2021

Object Segmentation Tracking

Object Segmentation Tracking from Generic Video Cues

Amirhossein Kardoost, Sabine Müller, Joachim Weickert, Margret Keuper

ICPR, 2021

Self-supervised Sparse to Dense Motion Segmentation

Self-supervised Sparse to Dense Motion Segmentation

Amirhossein Kardoost, Kalun Ho, Peter Ochs, Margret Keuper

ACCV, 2020

Two-Stage Minimum Cost Multicut

A Two-Stage Minimum Cost Multicut Approach to Self-Supervised Multiple Person Tracking

Kalun Ho, Amirhossein Kardoost, Franz-Josef Pfreundt, Janis Keuper, Margret Keuper

ACCV, 2020

Solving Minimum Cost Lifted Multicut

Solving Minimum Cost Lifted Multicut Problems by Node Agglomeration

Amirhossein Kardoost, Margret Keuper

ACCV, 2018