Code and Data

We present selected publications with available code and datasets to download.

Code

1. Complementary Time-Frequency Domain Networks for Dynamic Parallel MR Image Reconstruction
C. Qin, J. Duan, K. Hammernik, J. Schlemper, T. Küstner, R. Botnar, C. Prieto, A. N. Price, J. V. Hajnal, and D. Rueckert
TBA, submitted
Full Text Code

2. Convolutional Recurrent Neural Networks for Dynamic MR Image Reconstruction
C. Qin, J. Schlemper, J. Caballero, A.N. Price, J.V. Hajnal, and D. Rueckert
IEEE Transactions on Medical Imaging, vol. 38, 2019
Full Text Preprint Code

3. Biomechanics-Informed Neural Networks for Myocardial Motion Tracking in MRI
C. Qin, S. Wang, C. Chen, H. Qiu, W. Bai, and D. Rueckert.
MICCAI 2020
Full Text Preprint Code Website

4. Joint learning of motion estimation and segmentation for cardiac MR image sequences.
C. Qin, W. Bai, J. Schlemper, S. E. Petersen, S. K. Piechnik, S. Neubauer, and D. Rueckert
MICCAI 2018
Full Text Preprint Code Website

5. Learning to Segment from Scribbles using Multi-scale Adversarial Attention Gates
G. Valvano, A. Leo, S.A. Tsaftaris
IEEE Transactions on Medical Imaging,
Preprint Code Website

6. Pseudo-healthy synthesis with pathology disentanglement and adversarial learning
T. Xia, A. Chartsias, S.A. Tsaftaris
Medical Image Analysis, vol. 64, 2020
Full Text Preprint Code

7. Doing More with Less: A Multitask Deep Learning Approach in Plant Phenotyping
A. Dobrescu, M.V. Giuffrida, S.A. Tsaftaris
Frontiers in Plant Science, 11:141
Full Text Code

8. Blind Inpainting of Large-scale Masks of Thin Structures with Adversarial and Reinforcement Learning
H. Chen, M.V. Giuffrida, P. Doerner, S.A. Tsaftaris
TBA, submitted
Preprint Code

9. Learning to synthesise the ageing brain without longitudinal data
T. Xia, A. Chartsias, C. Wang, S.A. Tsaftaris
TBA, submitted
Preprint Code

10. Disentangle, align and fuse for multimodal and zero-shot image segmentation
A. Chartsias, G. Papanastasiou, C. Wang, S. Semple, D. Newby, R. Dharmakumar, S.A. Tsaftaris
IEEE Transactions on Medical Imaging, Volume: 40, Issue: 3, March 2021
Full Text Preprint Code

11. Unsupervised Rotation Factorization in Restricted Boltzmann Machines
V. Giuffrida, S.A. Tsaftaris
IEEE Transactions on Image Processing, vol. 29, no. 1, pp. 2166-2175, 2020
Full Text PDF Code

12. Disentangled Representation Learning in Cardiac Image Analysis
A. Chartsias, T. Joyce, G. Papanastasiou, S. Semple, M. Williams, D. Newby, R. Dharmakumar, S.A. Tsaftaris
Medical Image Analysis, vol. 58, 2019
Full Text Preprint Code

13. Multimodal MR Synthesis via Modality-Invariant Latent Representation
A. Chartsias, T. Joyce, V. Giuffrida, and S. A. Tsaftaris
IEEE Transactions on Medical Imaging, vol. 37, no. 3, pp. 803-814, 2018
Full Text PDF Code

14. Metrics for Exposing the Biases of Content-Style Disentanglement
X. Liu, S. Thermos, G. Valvano, A. Chartsias, A.Q. O'Neil, S.A. Tsaftaris
submitted
Preprint Code

15. INSIDE: Steering Spatial Attention with Non-Imaging Information in CNNs
G. Jacenków, A.Q. O'Neil, B. Mohr, S.A. Tsaftaris
MICCAI 2020
Full Text Preprint Code

16. Disentangled Representations for Domain-generalized Cardiac Segmentation
X. Liu, S. Thermos, A. Chartsias, A.Q. O'Neil, S.A. Tsaftaris
MICCAI 2020, STACOM: Statistical Atlases and Computational Modelling of the Heart
Preprint Code

17. Max-Fusion U-Net for Multi-Modal Pathology Segmentation with Attention and Dynamic Resampling
H. Jiang, C. Wang, A. Chartsias, S.A. Tsaftaris
MICCAI 2020, MyoPS: Multi-sequence CMR based Mycardial Pathology Segmentation Challenge
Preprint Code

18. Semi-supervised Pathology Segmentation with Disentangled Representations
H. Jiang, A. Chartsias, X. Zhang, G. Panastasiou, S. Semple, M. Dweck, D. Semple, R. Dharmakumar, S.A. Tsaftaris
MICCAI 2020, DART: Domain Adaptation and Representation Transfer
Preprint Code

19. Consistent Brain Ageing Synthesis
T. Xia, A. Chartsias, S.A. Tsaftaris
MICCAI 2019
PDF Code

20. Multimodal cardiac segmentation using disentangled representations
A. Chartsias, G. Papanastasiou, C. Wang, C. Stirrat, S. Semple, D. Newby, R. Dharmakumar, S.A. Tsaftaris
MICCAI 2019, STACOM: Statistical Atlases and Computational Models of the Heart
PDF Code

21. Temporal Consistency Objectives Regularize the Learning of Disentangled Representations
G. Valvano, A. Chartsias, A. Leo, S.A. Tsaftaris
MICCAI 2019, DART: Domain Adaptation and Representation Transfer
Preprint Code

22. Adversarial Pseudo Healthy Synthesis Needs Pathology Factorization
T. Xia, A. Chartsias, S.A. Tsaftaris
MIDL 2019
Full Text Code

23. Factorised spatial representation learning: application in semi-supervised myocardial segmentation
A. Chartsias, T. Joyce, G. Papanastasiou, S. Semple, M. Williams, D. Newby, R. Dharmakumar, S.A. Tsaftaris
MICCAI 2018
Preprint Code

24. Robust Multi-Modal MR Image Synthesis
T. Joyce, A. Chartsias, S.A. Tsaftaris
MICCAI 2017
PDF Code

25. Leveraging multiple datasets for deep leaf counting
A. Dobrescu, M.V. Giuffrida, S.A. Tsaftaris
ICCV 2017, CVPPP: Computer Vision Problems in Plant Phenotyping
PDF Code

Platforms

1. Phenotiki
Open source open hardware platform for affordable plant phenotyping, as of now has been downloaded by 100 users and is actively used by 30 labs in the world.
Full Text Website

Datasets

1. The PRL – CVPPP Dataset
A collection of annotated data for computer vision research in plant phenotyping, as of now it has been downloaded 3000 times, and cited 54 times.
Full Text Website
2. The CLEVR-Seg Dataset
Extension of the CLEVR dataset with segmentation masks and per-object attributes.
Full Text Code Website