Here we only list publications related to the activities of the group. For other publications of the lab members, please consult their personal pages.

2025

Learn2Reg 2024: New Benchmark Datasets Driving Progress on New Challenges
L. Hansen, W. Heyer, et al.
Forthcoming, 2025
arXiv preprint: arXiv.2509.01217

A Comparison of Deep Learning Methods for Cell Detection in Digital Cytology
M. Acerbis, N. Sladoje, J. Lindblad
In: Scandinavian Conference on Image Analysis (SCIA), Lecture Notes in Computer Science (LNCS), Vol. 15726, 2025, doi: 10.1007/978-3-031-95918-9_19
arXiv preprint: arXiv.2504.06957
Code available at github.com/MIDA-group/Cell-Detection

Isolated Channel Vision Transformers: From Single-Channel Pretraining to Multi-Channel Finetuning
W. Lian, J. Lindblad, P. Micke, N. Sladoje
In: British Machine Vision Conference (BMVC), 2025, Accepted
arXiv preprint: arXiv.2503.09826

Let it shine: Autofluorescence of Papanicolaou-stain improves AI-based cytological oral cancer detection
W. Lian, J. Lindblad, C. Runow Stark, J-M. Hirsch, N. Sladoje
Computers in Biology and Medicine, Vol. 185, 109498, 2025, doi: 10.1016/j.compbiomed.2024.109498
arXiv preprint: arXiv.2407.01869
Code available at github.com/MIDA-group/LetItShine

Roadmap on deep learning for microscopy
G. Volpe, C. Wählby, L. Tian et al.
Journal of Physics: Photonics, 2025, doi: 10.1088/2515-7647/ae0fd1

UpStory: the uppsala storytelling dataset
M. Fraile, N. Calvo-Barajas, A. S. Apeiron, G. Varni, J. Lindblad, N. Sladoje, G. Castellano
Frontiers in robotics and AI, Vol. 12(1547578), 2025, doi: 10.3389/frobt.2025.1547578
arXiv preprint: arXiv.2407.04352
Code available at github.com/MarcFraile/dyadic-storytelling
Data available at doi.org/10.5281/zenodo.15391848

2024

Cross-modality sub-image retrieval using contrastive multimodal image representations
E. Breznik, E. Wetzer, J. Lindblad, N. Sladoje
Scientific Reports, Vol. 14, 18798, 2024, doi: 10.1038/s41598-024-68800-1
arXiv preprint: arXiv.2201.03597
Code available at github.com/MIDA-group/CrossModal_ImgRetrieval

Deep multiple instance learning versus conventional deep single instance learning for interpretable oral cancer detection
N. Koriakina, N. Sladoje, V. Bašić, J. Lindblad
PLoS ONE, Vol. 19(4), e0302169, 2024, doi: 10.1371/journal.pone.0302169
arXiv preprint: arXiv.2202.01783
Code available at github.com/MIDA-group/OralCancerMILvsSIL
Data available at doi.org/10.5281/zenodo.7020311

Detection of Extremely Sparse Key Instances in Whole Slide Cytology Images via Self-supervised One-class Representation Learning
S. Chatterjee, O. Göksel, N. Sladoje, J. Lindblad
In: International Conference on Pattern Recognition, ICPR 2024, Lecture Notes in Computer Science (LNCS), Vol. 15327, 2024, doi: 10.1007/978-3-031-78398-2_27
Code available at github.com/MIDA-group/occ_cyto

Are We Friends? End-to-End Prediction of Child Rapport in Guided Play
M. Fraile, G. Varni, J. Lindblad, N. Sladoje, G. Castellano
In: European Conference on Computer Vision, ECCV 2004 Workshops, Lecture Notes in Computer Science (LNCS), Vol. 15637, 2024, doi: 10.1007/978-3-031-91581-9_27

Correlated multimodal imaging in life sciences: lessons learnt
P. S. Rudraiah, R. Camacho, et al.
Frontiers in Biomaterials Science, Vol. 3, 2024, doi: 10.3389/fbiom.2024.1338115

Early Detection of Oral Potentially Malignant Disorders: A Review on Prospective Screening Methods with Regard to Global Challenges
N. Haj-Hosseini, J. Lindblad, B. Hasséus, V.V. Kumar, N. Subramaniam, J-M. Hirsch
Journal of Maxillofacial and Oral Surgery, Vol. 23, 2024, doi: 10.1007/s12663-022-01710-9

2023

Bio-Image Informatics Index BIII: A unique database of image analysis tools and workflows for and by the bioimaging community
C. Zhang, A. Gaignard et al.
Submitted, 2023
arXiv preprint: arXiv.2312.11256

Automated detection, segmentation and measurement of major vessels and the trachea in CT pulmonary angiography
A. T. Kahraman, T. Fröding, D. Toumpanakis, N. Sladoje, T. Sjöblum
Scientific Reports, Vol. 13, 18407, 2023, doi: 10.1038/s41598-023-45509-1

Can Representation Learning for Multimodal Image Registration be Improved by Supervision of Intermediate Layers?
E. Wetzer, J. Lindblad, N. Sladoje
In: Iberian Conference on Pattern Recognition and Image Analysis, IbPRIA 2023, Lecture Notes in Computer Science (LNCS), Vol. 14062, 2023, doi: 10.1007/978-3-031-36616-1_21
arXiv preprint: arXiv.2303.00403

A paradigm shift in the prevention and diagnosis of oral squamous cell carcinoma
J-M. Hirsch, R. Sandy, B. Hasséus, J. Lindblad
Journal of Oral Pathology & Medicine, Vol. 52(9), 2023, doi: 10.1111/jop.13484

Dental hygienists and dentists as providers of brush biopsies for oral mucosa screening
K. Edman, C. Runow Stark, V. Basic, J. Lindblad, J-M. Hirsch
International Journal of Dental Hygiene, Vol. 21(3), 2023, doi: 10.1111/idh.12713

Contrastive Learning of Equivariant Image Representations for Multimodal Deformable Registration
L. Nordling, J. Öfverstedt, J. Lindblad, N. Sladoje
In: IEEE 20th International Symposium on Biomedical Imaging, ISBI 2023, 2023, doi: 10.1109/ISBI53787.2023.10230465
Code available at github.com/MIDA-group/CoMIR_INSPIRE

INSPIRE: Intensity and spatial information-based deformable image registration
J. Öfverstedt, J. Lindblad, N. Sladoje
PLoS ONE, Vol. 18(3), e0282432, 2023, doi: 10.1371/journal.pone.0282432
Code available at github.com/MIDA-group/inspire
Data available at 10.5281/zenodo.7552884

2022

End-to-end Multiple Instance Learning with Gradient Accumulation
A. Andersson, N. Koriakina, N. Sladoje, J. Lindblad
In: IEEE International Conference on Big Data, 2022, 2022, doi: 10.1109/BigData55660.2022.10020801
arXiv preprint: arXiv.2203.03981
Code available at github.com/axanderssonuu/ABMIL_with_accumulating_gradients

Fast computation of mutual information in the frequency domain with applications to global multimodal image alignment
J. Öfverstedt, J. Lindblad, N. Sladoje
Pattern Recognition Letters, Vol. 159, 2022, doi: 10.1016/j.patrec.2022.05.022
arXiv preprint: arXiv.2106.14699
Code available at github.com/MIDA-group/globalign

Cross-Sim-NGF: FFT-Based Global Rigid Multimodal Alignment of Image Volumes using Normalized Gradient Fields
J. Öfverstedt, J. Lindblad, N. Sladoje
In: 10th International Workshop on Biomedical Image Registration (WBIR), Lecture Notes in Computer Science (LNCS), Vol. 13386, 2022, doi: 10.1007/978-3-031-11203-4_17
arXiv preprint: arXiv.2110.10156
Code available at github.com/mida-group/cross_sim_ngf

End-to-End Learning and Analysis of Infant Engagement During Guided Play: Prediction and Explainability
M. Fraile, C. Fawcett, J. Lindblad, N. Sladoje, G. Castellano
In: 24th ACM International Conference on Multimodal Interaction, ICMI 2022, 2022, doi: 10.1145/3536221.3556629
Code available at github.com/MarcFraile/infant-engagement

Is Image-to-Image Translation the Panacea for Multimodal Image Registration? A Comparative Study
J. Lu, J. Öfverstedt, J. Lindblad, N. Sladoje
PLoS ONE, Vol. 17(11), e0276196, 2022, doi: 10.1371/journal.pone.0276196
arXiv preprint: arXiv.2103.16262
Code available at github.com/MIDA-group/MultiRegEval

Rotation-Equivariant Semantic Instance Segmentation on Biomedical Images
K. Bengtsson Bernander, J. Lindblad, R. Strand, I. Nyström
In: 26th Conference on Medical Image Understanding and Analysis (MIUA), Lecture Notes in Computer Science (LNCS), Vol. 13413, 2022, doi: 10.1007/978-3-031-12053-4_22

Special Issue on Discrete Geometry and Mathematical Morphology, Guest Editorial
F. Malmberg, J. Lindblad, N. Sladoje, Editors
Journal of Mathematical Imaging and Vision, Vol. 67(7), 2022, doi: 10.1007/s10851-022-01117-8