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Empirical Evaluation of Deep Learning Approaches for Landmark Detection in Fish Bioimages
Kumar, Navdeep  ; Claudia Di Biagio; Zachary Dellacqua et al.
In press
 

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Keywords :
Deep Learning, Multi-modal image analysis, landmark detection, artificial intelligence, bio images, fish
Abstract :
[en] In this paper we perform an empirical evaluation of variants of deep learning methods to automatically localize anatomical landmarks in bioimages of fishes acquired using different imaging modalities (microscopy and radiography). We compare two methodologies namely heatmap based regression and multivariate direct regression, and evaluate them in combination with several Convolutional Neural Network (CNN) architectures. Heatmap based regression approaches employ Gaussian or Exponential heatmap generation functions combined with CNNs to output the heatmaps corresponding to landmark locations whereas direct regression approaches output directly the (x, y) coordinates corresponding to landmark locations. In our experiments, we use two microscopy datasets of Zebrafish and Medaka fish and one radiography dataset of gilthead Seabream. On our three datasets, the heatmap approach with Exponential function and U-Net architecture performs better. Datasets and open-source code for training and prediction are made available to ease future landmark detection research and bioimaging applications.
Disciplines :
Computer science
Human health sciences: Multidisciplinary, general & others
Author, co-author :
Kumar, Navdeep ;  Université de Liège - ULiège > Montefiore Institute of Electrical Engineering and Computer Science
Claudia Di Biagio;  University of Rome Tor Vergata > Biology
Zachary Dellacqua;  University of Rome Tor Vergata > Biology
Raman, Ratish ;  Université de Liège - ULiège > GIGA
Arianna Martini;  CREA - Council for Agricultural Research and Economics Research Centre for Animal Production and Aquaculture
Clara Boglione;  University of Rome Tor Vergata > Biology
Muller, Marc  ;  Université de Liège - ULiège > GIGA > GIGA I3 - Laboratory for Organogenesis and Regeneration
Geurts, Pierre ;  Université de Liège - ULiège > Montefiore Institute of Electrical Engineering and Computer Science
Marée, Raphaël  ;  Université de Liège - ULiège > Montefiore Institute of Electrical Engineering and Computer Science
Language :
English
Title :
Empirical Evaluation of Deep Learning Approaches for Landmark Detection in Fish Bioimages
Publication date :
In press
Event name :
Bio Image Computing Workshop in European Conference on Computer Vision 2022
Event place :
Tel Aviv, Israel
Event date :
23-27 October
Audience :
International
Development Goals :
2. Zero hunger
3. Good health and well-being
9. Industry, innovation and infrastructure
European Projects :
H2020 - 766347 - BioMedaqu - Aquaculture meets Biomedicine: Innovation in Skeletal Health research.
Funders :
EC - European Commission [BE]

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