Research & Papers
Marta K. Skrok, Robert Konklewski, Patrycjusz Stremplewski, Maciej Nowakowski, Szymon Tamborski, Valentyna Pryhodiuk, Jakub Lipiński, Michał Meina, Marcus Nyström, Ignace T. C. Hooge, Diederick C. Niehorster, Anna Szkulmowska & Maciej Szkulmowski
Scientific Reports, published online 17 September 2026
Eye-tracking is increasingly prevalent across various aspects of our lives. It is currently used for research, education, diagnostics, and entertainment, for example, in virtual reality goggles. However, widely used video-based eye-trackers require subject-dependent calibration, which makes them unsuitable for examining individuals with unstable fixation, such as patients with neurodegenerative diseases. We present a novel calibration-free retinal-anterior eye tracker that uses retinal images to track changes in eye orientation. On an artificial eye, the eye tracker achieves an accuracy better than 0.6′ (0.01°) and a sample-to-sample precision of 0.09′ (0.0015°) for the reference-frame signal, improving to 0.05′ (0.0008°) after Kalman fusion. Under similar conditions, this precision exceeds that reported for video-based eye trackers. After a one-point trajectory offset correction, the eye tracker enables determination of the absolute gaze direction. The eye-tracker was tested with an artificial eye over a traverse of −8° to +8°. In human recordings we typically work within approximately ±4°, a practical limit based on operating experience rather than on a systematic characterization. The eye-tracker is capable of measuring saccadic velocities of up to 300°/s, incorporates an integrated display for dynamic stimulus presentation, and requires only a simple chin- and forehead rest for subject stabilization. The potential of this eye-tracker is demonstrated in healthy subjects and in participants who are unable to undergo a conventional calibration procedure. Additionally, the device is equipped with a synchronized video-based eye-tracker, making it a powerful research platform for developing eye-tracking technologies.
https://doi.org/10.1038/s41598-026-70924-5
Marcus Nyström, Diederick C. Niehorster, Roy S. Hessels, Richard Andersson, Marta K. Skrok, Robert Konklewski, Patrycjusz Stremplewski, Maciej Nowakowski, Jakub Lipiński, Szymon Tamborski, Anna Szkulmowska, Maciej Szkulmowski & Ignace T. C. Hooge
Behavior Research Methods, Volume 57, article number 329, (2025)
The eyeball is not rigid and deforms during saccades. As a consequence, the saccade waveform recorded by an eye tracker may depend on which structure of the eye is used to estimate eyeball rotation. Here, we systematically describe and compare signals co-recorded from the retina, the cornea (corneal reflection, CR), the pupil, and the lens (fourth Purkinje reflection, P4) during saccades. We found that several commonly used parameters for saccade characterization differ systematically across the signals. For instance, saccades in the retinal signal had earlier onsets compared to saccades in the pupil and the P4 signals. The retinal signal had the smallest saccade amplitude and reached the peak saccade velocity earlier compared to the other signals. At the end of saccades, the retinal signal came to a stop faster than the other signals. We discuss possible explanations that may account for the relationship between the retinal signal and the other signals.
https://doi.org/10.3758/s13428-025-02862-5
Maciej Szkulmowski, Marta K. Skrok, Robert Konklewski, Patrycjusz Stremplewski, Maciej Nowakowski, Szymon Tamborski, Valentyna Pryhodiuk, Jakub Lipiński, Marcus Nyström, Ignace T. C. Hooge, Diederick C. Niehorster & Anna Szkulmowska
Investigative Ophthalmology & Visual Science, June 2025, Vol. 66, Issue 8, 5353 (ARVO Annual Meeting Abstract, Salt Lake City, May 4–8, 2025)
Purpose: Dual Purkinje Image (DPI) and Pupil-Corneal Reflection (PCR) eye trackers are widely used in eye movement research and for early diagnostics of vision and neurological diseases. They have limited accuracy and precision due to individual differences and nonlinear relations between eye rotation and displacement of the lens, pupil, or cornea. They also suffer from artifacts such as lens wobbling or displacement of the pupil center during accommodation or pupil dilation. The purpose of this study is to simultaneously register the images from the retina and the front of the eye during fixations, saccades, and smooth pursuit, to compare the differences between the features of signals registered by the two technologies and find limits of their applicability in research and diagnostics. Methods: The experimental setup consists of a high-speed CMOS camera that acquires images of the anterior part of the eye with Purkinje reflections and a confocal scanning microscope optimized for retinal imaging. The system presents visual tasks created with PsychoPy software with an LCD display. The accuracy and precision of the prototype were measured using an artificial eye. 150 subjects aged 25-70 were examined with fixation, saccades, and smooth pursuit tasks. Recorded eye movement trajectories were divided into saccades and drift periods and analyzed separately. Results: Artificial eye measurement shows precision below 0.03 arcmin and accuracy ranging from 0.2 arcmins for saccades with 1 arcmin amplitude to <2 arcmins for 8deg saccades. This was confirmed on human data with retinal tracker precision measured as 0.04 arcmin. The precision of the DPI tracker was measured to be 1 arcmin, and the PCR tracker was almost 8 arcmin. The simultaneous registration of two signals from different parts of the eye revealed strong differences; for example, saccadic velocity and amplitudes measured by the DPI tracker were 1.7 to over 3 times higher than for the retinal tracker, depending on the subject. Conclusions: The retinal eye tracker can register eye movements during psychophysical tasks with accuracy and precision significantly exceeding the classical eye trackers. A direct comparison of the results shows that the classical eye trackers not only offer inferior precision to the retinal tracker but are also burdened with artifacts that can impede their use in medical applications.
https://iovs.arvojournals.org/article.aspx?articleid=2808673
Maciej Szkulmowski, Marta K. Skrok, Robert Konklewski, Patrycjusz Stremplewski, Maciej Nowakowski, Valentyna Pryhodiuk, Jakub Lipiński, Marcus Nyström, Ignace T. C. Hooge, Diederick C. Niehorster & Anna Szkulmowska
Proc. SPIE PC13300, Ophthalmic Technologies XXXV, PC1330009 (3 April 2025); SPIE BiOS, San Francisco, 25–31 January 2025
An eye-tracking device with combined retinal and anterior eye-tracking capabilities
Understanding how the eye moves is of utmost importance to scientists in neurology, ophthalmology, cognitive sciences, and medicine. Popular eye trackers observe the anterior parts of the eye, but a new class of eye-trackers looks at the retina. Each of the two techniques has advantages and disadvantages: the anterior eye trackers provide data with low precision but high accuracy, while retinal eye trackers provide data with high precision but low accuracy. We have built a device that combines the two trackers and allows for the simultaneous acquisition of eye motion on the anterior and posterior parts of the eye during visual tasks displayed to the subject, such as fixations, saccades, and smooth pursuit. The retinal tracker is based on the concept of SLO, but modified to acquire small image frames (5deg x 3deg) at high speeds. The anterior tracker uses a CMOS camera to register the pupil and the Purkinje reflections.
https://doi.org/10.1117/12.3047812
Mateusz Chiliński, Jakub Lipiński, Abhishek Agarwal, Yijun Ruan, Dariusz Plewczynski
Scientific Reports volume 13, Article number: 11693 (2023)
There have been multiple attempts to predict the expression of the genes based on the sequence, epigenetics, and various other factors. To improve those predictions, we have decided to investigate adding protein-specific 3D interactions that play a significant role in the condensation of the chromatin structure in the cell nucleus. To achieve this, we have used the architecture of one of the state-of-the-art algorithms, ExPecto, and investigated the changes in the model metrics upon adding the spatially relevant data. We have used ChIA-PET interactions that are mediated by cohesin (24 cell lines), CTCF (4 cell lines), and RNAPOL2 (4 cell lines). As the output of the study, we have developed the Spatial Gene Expression (SpEx) algorithm that shows statistically significant improvements in most cell lines. We have compared ourselves to the baseline ExPecto model, which obtained a 0.82 Spearman’s rank correlation coefficient (SCC) score, and 0.85, which is reported by newer Enformer were able to obtain the average correlation score of 0.83. However, in some cases (e.g. RNAPOL2 on GM12878), our improvement reached 0.04, and in some cases (e.g. RNAPOL2 on H1), we reached an SCC of 0.86.
https://doi.org/10.1038/s41598-023-38865-5
Cheynna Crowley, Yuchen Yang, Yunjiang Qiu, Benxia Hu, Armen Abnousi, Jakub Lipiński, Dariusz Plewczyński, Di Wu, Hyejung Won, Bing Ren, Ming Hu, Yun Li,
Computational and Structural Biotechnology Journal 2020, ISSN 2001-0370
FIREcaller: Detecting Frequently Interacting Regions from Hi-C Data
Abstract: Hi-C experiments have been widely adopted to study chromatin spatial organization, which plays an essential role in genome function. We have recently identified frequently interacting regions (FIREs) and found that they are closely associated with cell-type-specific gene regulation. However, computational tools for detecting FIREs from Hi-C data are still lacking. In this work, we present FIREcaller, a stand-alone, user-friendly R package for detecting FIREs from Hi-C data. FIREcaller takes raw Hi-C contact matrices as input, performs within-sample and cross-sample normalization, and outputs continuous FIRE scores, dichotomous FIREs, and super-FIREs. Applying FIREcaller to Hi-C data from various human tissues, we demonstrate that FIREs and super-FIREs identified, in a tissue-specific manner, are closely related to gene regulation, are enriched for enhancer-promoter (E-P) interactions, tend to overlap with regions exhibiting epigenomic signatures of cis-regulatory roles, and aid the interpretation or GWAS variants.