Sepideh Hatamikia

Prof. Sepideh Hatamikia

1. Computational Imaging, Research Center MIAAI (Medical Image Analysis & Artificial Intelligence), Faculty of Medicine/Dentistry, Danube Private University, Krems-Stein, Austria
+1

Research Focus & Metrics

Academic Career Length

7Years (2020-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

View All Publications
16 August 2022 in Physics in Medicine & Biology
Verified
Journal Article
Open access
Sepideh HatamikiaSepideh Hatamikia
Sepideh Hatamikia
ABAnder Biguri
Ander Biguri
GHG Herl
G Herl
GKG Kronreif
G Kronreif
TRT Reynolds
T Reynolds
WBW Birkfellner
W Birkfellner
Cone-beam computed tomography (CBCT) imaging is becoming increasingly important for a wide range of applications such as image-guided surgery, image-guided radiation therapy as well as diagnostic imaging such as breast and orthopaedic imaging. The potential benefits of non-circular source-detector trajectories was recognized in early work to improve the completeness of CBCT sampling and extend the field of view (FOV). Another important feature of interventional imaging is that prior knowledge of patient anatomy such as a preoperative CBCT or prior CT is commonly available. This provides the opportunity to integrate such prior information into the image acquisition process by customized CBCT source-detector trajectories. Such customized trajectories can be designed in order to optimize task-specific imaging performance, providing intervention or patient-specific imaging settings. The recently developed robotic CBCT C-arms as well as novel multi-source CBCT imaging systems with additional degrees of freedom provide the possibility to largely expand the scanning geometries beyond the conventional circular source-detector trajectory. This recent development has inspired the research community to innovate enhanced image quality by modifying image geometry, as opposed to hardware or algorithms. The recently proposed techniques in this field facilitate image quality improvement, FOV extension, radiation dose reduction, metal artifact reduction as well as 3D imaging under kinematic constraints. Because of the great practical value and the increasing importance of CBCT imaging in image-guided therapy for clinical and preclinical applications as well as in industry, this paper focuses on the review and discussion of the available literature in the CBCT trajectory optimization field. To the best of our knowledge, this paper is the first study that provides an exhaustive literature review regarding customized CBCT algorithms and tries to update the community with the clarification of in-depth information on the current progress and future trends.

13 September 2023 in European Radiology Experimental
Verified
Journal Article
Open access
PDF file
Sepideh HatamikiaSepideh Hatamikia
Sepideh Hatamikia
SNStephanie Nougaret
Stephanie Nougaret
CPCamilla Panico
Camilla Panico
GAGiacomo Avesani
Giacomo Avesani
CNCamilla Nero
Camilla Nero
RWRamona Woitek
Ramona Woitek
High-grade serous ovarian cancer is the most lethal gynaecological malignancy. Detailed molecular studies have revealed marked intra-patient heterogeneity at the tumour microenvironment level, likely contributing to poor prognosis. Despite large quantities of clinical, molecular and imaging data on ovarian cancer being accumulated worldwide and the rise of high-throughput computing, data frequently remain siloed and are thus inaccessible for integrated analyses. Only a minority of studies on ovarian cancer have set out to harness artificial intelligence (AI) for the integration of multiomics data and for developing powerful algorithms that capture the characteristics of ovarian cancer at multiple scales and levels. Clinical data, serum markers, and imaging data were most frequently used, followed by genomics and transcriptomics. The current literature proves that integrative multiomics approaches outperform models based on single data types and indicates that imaging can be used for the longitudinal tracking of tumour heterogeneity in space and potentially over time. This review presents an overview of studies that integrated two or more data types to develop AI-based classifiers or prediction models.Relevance statement Integrative multiomics models for ovarian cancer outperform models using single data types for classification, prognostication, and predictive tasks.Key points• This review presents studies using multiomics and artificial intelligence in ovarian cancer.• Current literature proves that integrative multiomics outperform models using single data types.• Around 60% of studies used a combination of imaging with clinical data.• The combination of genomics and transcriptomics with imaging data was infrequently used. Graphical Abstract

16 April 2025 in Frontiers in Medicine
Verified
Journal Article
Open access
PDF file
ABArezoo Borji
Arezoo Borji
GKGernot Kronreif
Gernot Kronreif
BABernhard Angermayr
Bernhard Angermayr
Sepideh HatamikiaSepideh Hatamikia
Sepideh Hatamikia
Background: Recent advances in machine learning are transforming medical image analysis, particularly in cancer detection and classification. Techniques such as deep learning, especially convolutional neural networks (CNNs) and vision transformers (ViTs), are now enabling the precise analysis of complex histopathological images, automating detection, and enhancing classification accuracy across various cancer types. This study focuses on osteosarcoma (OS), the most common bone cancer in children and adolescents, which affects the long bones of the arms and legs. Early and accurate detection of OS is essential for improving patient outcomes and reducing mortality. However, the increasing prevalence of cancer and the demand for personalized treatments create challenges in achieving precise diagnoses and customized therapies.Methods: We propose a novel hybrid model that combines convolutional neural networks (CNN) and vision transformers (ViT) to improve diagnostic accuracy for OS using hematoxylin and eosin (H&E) stained histopathological images. The CNN model extracts local features, while the ViT captures global patterns from histopathological images. These features are combined and classified using a Multi-Layer Perceptron (MLP) into four categories: non-tumor (NT), non-viable tumor (NVT), viable tumor (VT), and non-viable ratio (NVR).Results: Using the Cancer Imaging Archive (TCIA) dataset, the model achieved an accuracy of 99.08%, precision of 99.10%, recall of 99.28%, and an F1-score of 99.23%. This is the first successful four-class classification using this dataset, setting a new benchmark in OS research and offering promising potential for future diagnostic advancements.

24 February 2022 in Zeitschrift für Medizinische Physik
Verified
Journal Article
Open access
Sepideh HatamikiaSepideh Hatamikia
Sepideh Hatamikia
GKGernot Kronreif
Gernot Kronreif
AUAlexander Unger
Alexander Unger
GOGunpreet Oberoi
Gunpreet Oberoi
LJLaszlo Jaksa
Laszlo Jaksa
ALAndrea Lorenz
Andrea Lorenz
Current medical imaging phantoms are usually limited by simplified geometry and radiographic skeletal homogeneity, which confines their usage for image quality assessment. In order to fabricate realistic imaging phantoms, replication of the entire tissue morphology and the associated CT numbers, defined as Hounsfield Unit (HU) is required. 3D printing is a promising technology for the production of medical imaging phantoms with accurate anatomical replication. So far, the majority of the imaging phantoms using 3D printing technologies tried to mimic the average HU of soft tissue human organs. One important aspect of the anthropomorphic imaging phantoms is also the replication of realistic radiodensities for bone tissues. In this study, we used filament printing technology to develop a CT-derived 3D printed thorax phantom with realistic bone-equivalent radiodensity using only one single commercially available filament. The generated thorax phantom geometry closely resembles a patient and includes direct manufacturing of bone structures while creating life-like heterogeneity within bone tissues. A HU analysis as well as a physical dimensional comparison were performed in order to evaluate the density and geometry agreement between the proposed phantom and the corresponding CT data. With the achieved density range (-482 to 968 HU) we could successfully mimic the realistic radiodensity of the bone marrow as well as the cortical bone for the ribs, vertebral body and dorsal vertebral column in the thorax skeleton. In addition, considering the large radiodensity range achieved a full thorax imaging phantom mimicking also soft tissues can become feasible. The physical dimensional comparison using both Extrema Analysis and Collision Detection methods confirmed a mean surface overlap of 90% and a mean volumetric overlap of 84,56% between the patient and phantom model. Furthermore, the reproducibility analyses revealed a good geometry and radiodensity duplicability in 24 printed cylinder replicas. Thus, according to our results, the proposed additively manufactured anthropomorphic thorax phantom has the potential to be efficiently used for validation of imaging- and radiation-based procedures in precision medicine.

1 April 2025 in European Journal of Radiology
Verified
Journal Article
Open access
FSFlorian Schwarzhans
Florian Schwarzhans
GGGeevarghese George
Geevarghese George
LSLorena Escudero Sanchez
Lorena Escudero Sanchez
OZOlgica Zaric
Olgica Zaric
JAJean E. Abraham
Jean E. Abraham
Sepideh HatamikiaSepideh Hatamikia
Sepideh Hatamikia
Radiomics analysis has emerged as a promising approach to aid in cancer diagnosis and treatment. However, radiomics research currently lacks standardization, and radiomics features can be highly dependent on acquisition and pre-processing techniques used. In this study, we aim to investigate the effect of various image normalization techniques on robustness of radiomics features extracted from breast cancer patient MRI scans. MRI scans from the publicly available MAMA-MIA dataset and an internal breast MRI test set depicting triple negative breast cancer (TNBC) were used. We compared the effect of commonly used image normalization techniques on radiomics feature robustnessusing Concordance-Correlation-Coefficient (CCC) between multiple combinations of normalization approaches. We also trained machine learning-based prediction models of pathologic complete response (pCR) on radiomics after different normalization techniques were used and compared their areas under the receiver operating characteristic curve (ROC-AUC). For predicting complete pathological response from pre-treatment breast cancer MRI radiomics, the highest overall ROC-AUC was achieved by using a combination of three different normalization techniques indicating their potentially powerful role when working with heterogeneous imaging data. The effect of normalization was more pronounced with smaller training data and normalization may be less important with increasing abundance of training data. Additionally, we observed considerable differences between MRI data sets and their feature robustness towards normalization. Overall, we were able to demonstrate the importance of selecting and standardizing normalization methods for accurate and reliable radiomics analysis in breast MRI scans especially with small training data sets.

17 July 2020 in Medical Physics
Verified
Journal Article
Open access
PDF file
Sepideh HatamikiaSepideh Hatamikia
Sepideh Hatamikia
ABAnder Biguri
Ander Biguri
GKGernot Kronreif
Gernot Kronreif
JKJoachim Kettenbach
Joachim Kettenbach
TRTom Russ
Tom Russ
WBWolfgang Birkfellner
Wolfgang Birkfellner
Purpose: We developed a target‐based cone beam computed tomography (CBCT) imaging framework for optimizing an unconstrained three dimensional (3D) source‐detector trajectory by incorporating prior image information. Our main aim is to enable a CBCT system to provide topical information about the target using a limited angle noncircular scan orbit with a minimal number of projections. Such a customized trajectory should include enough information to sufficiently reconstruct a particular volume of interest (VOI) under kinematic constraints, which may result from the patient size or additional surgical or radiation therapy‐related equipment.Methods: A patient‐specific model from a prior diagnostic computed tomography (CT) volume is used as a digital phantom for CBCT trajectory simulations. Selection of the best projection views is accomplished through maximizing an objective function fed by the imaging quality provided by different x‐ray positions on the digital phantom data. The final optimized trajectory includes a limited angular range and a minimal number of projections which can be applied to a C‐arm device capable of general source‐detector positioning. The performance of the proposed framework is investigated in experiments involving an in‐house‐built box phantom including spherical targets as well as an Alderson‐Rando head phantom. In order to quantify the image quality of the reconstructed image, we use the average full‐width‐half‐maximum (FWHMavg) for the spherical target and feature similarity index (FSIM), universal quality index (UQI), and contrast‐to‐noise ratio (CNR) for an anatomical target.Results: Our experiments based on both the box and head phantom showed that optimized trajectories could achieve a comparable image quality in the VOI with respect to the standard C‐arm circular CBCT while using approximately one quarter of projections. We achieved a relative deviation <7% for FWHMavg between the reconstructed images from the optimized trajectories and the standard C‐arm CBCT for all spherical targets. Furthermore, for the anatomical target, the relative deviation of FSIM, UQI, and CNR between the reconstructed image related to the proposed trajectory and the standard C‐arm circular CBCT was found to be 5.06%, 6.89%, and 8.64%, respectively. We also compared our proposed trajectories to circular trajectories with equivalent angular sampling as the optimized trajectories. Our results show that optimized trajectories can outperform simple partial circular trajectories in the VOI in term of image quality. Typically, an angular range between 116° and 152° was used for the optimized trajectories.Conclusion: We demonstrated that applying limited angle noncircular trajectories with optimized orientations in 3D space can provide a suitable image quality for particular image targets and has a potential for limited angle and low‐dose CBCT‐based interventions under strong spatial constraints.