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  4. Self-supervised Dense Representation Learning for Live-Cell Microscopy with Time Arrow Prediction
 
conference paper

Self-supervised Dense Representation Learning for Live-Cell Microscopy with Time Arrow Prediction

Gallusser, Benjamin  
•
Stieber, Max
•
Weigert, Martin  
Greenspan, H
•
Madabhushi, A
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January 1, 2023
Medical Image Computing And Computer Assisted Intervention, Miccai 2023, Pt Viii
26th International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI)

State-of-the-art object detection and segmentation methods for microscopy images rely on supervised machine learning, which requires laborious manual annotation of training data. Here we present a self-supervised method based on time arrow prediction pre-training that learns dense image representations from raw, unlabeled live-cell microscopy videos. Our method builds upon the task of predicting the correct order of time-flipped image regions via a single-image feature extractor followed by a time arrow prediction head that operates on the fused features. We show that the resulting dense representations capture inherently time-asymmetric biological processes such as cell divisions on a pixel-level. We furthermore demonstrate the utility of these representations on several live-cell microscopy datasets for detection and segmentation of dividing cells, as well as for cell state classification. Our method outperforms supervised methods, particularly when only limited ground truth annotations are available as is commonly the case in practice. We provide code at https://github.com/weigertlab/tarrow.

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Type
conference paper
DOI
10.1007/978-3-031-43993-3_52
Web of Science ID

WOS:001109637500052

Author(s)
Gallusser, Benjamin  
Stieber, Max
Weigert, Martin  
Editors
Greenspan, H
•
Madabhushi, A
•
Mousavi, P
•
Salcudean, S
•
Duncan, J
•
Syeda-Mahmood, T
•
Taylor, R
Date Issued

2023-01-01

Publisher

Springer International Publishing Ag

Publisher place

Cham

Published in
Medical Image Computing And Computer Assisted Intervention, Miccai 2023, Pt Viii
ISBN of the book

978-3-031-43992-6

978-3-031-43993-3

Volume

14227

Start page

537

End page

547

Subjects

Technology

•

Life Sciences & Biomedicine

•

Self-Supervised Learning

•

Live-Cell Microscopy

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
GR-WEIGERT  
Event nameEvent placeEvent date
26th International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI)

Vancouver, CANADA

OCT 08-12, 2023

FunderGrant Number

EPFL School of Life Sciences ELISIR program

CARIGEST SA

Available on Infoscience
February 20, 2024
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/204691
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