16.12.2024

Ultrahigh resolution OCT

Some applications require finer imaging resolution. In optical coherence tomography (OCT), the transversal resolution is determined by imaging optics (often with working distance limitations), while axial resolution depends on the effective bandwidth of the light source. We developed a dual spectrometer spectral OCT system working with a broadband femtosecond laser as a source. The system provides a voxel resolution of approximately 2 micrometers.

We utilize the system for various applications, ranging from ex vivo imaging of biological samples (e.g., cornea, bladder tissue, mouse brain) to bioprinted materials (such as porous materials or muscles). In the latter application, we collaborate with Professor Marco Constantini from IPC PAS, who is always impressed with the technology’s capabilities.

More recently, we have begun developing elastography measurements with our system. The sample is compressed (at levels not visible in structural images) between measurements, and through analysis of differential phase information, we can provide contrast that depends on tissue mechanical properties. Since our dual spectrometer system also offers polarization contrast, we aim to investigate in the future whether these two types of contrasts are equivalent or complementary to each other.

Text: Karol Karnowski, PhD, Acting IDoc Leader

Project team:

Karol Karnowski

Piotr Kasprzycki

Patricio Espinoza

Wiktor Kulesza

Related funding: NAWA – Polish Returns, FNP – IRAP (MAB)

References:

  1.  M. Marcotulli, M. C. Tirelli, M. Volpi, J. Jaroszewicz, C. Scognamiglio, P. Kasprzycki, K. Karnowski, W. Święszkowski, G. Ruocco, M. Costantini, G. Cidonio, A. Barbetta, Microfluidic 3D Printing of Emulsion Ink for Engineering Porous Functionally Graded Materials. Adv. Mater. Technol. 2023, 8, 2201244
16.12.2024

Scanning OCT system for animal model study

Our collaborative research with ICTER focuses on advancing vision restoration therapies and fundamental investigations of retinal function using animal models. The team has already established a sophisticated Full-field Optical Coherence Tomography (FF-OCT) system specifically designed for mouse model imaging, capable of capturing both structural and functional retinal characteristics with exceptional precision.

To support the critical retinal injection procedures essential for therapeutic interventions, we are developing an advanced 1060 nm swept-source OCT system. This innovative imaging platform will serve multiple crucial functions, primarily providing real-time image guidance for automated eye injections. Beyond its primary injection support role, the system offers additional versatility by functioning as a comprehensive preview and eye alignment mechanism for our Full-field OCT research studies.

The 1060 nm wavelength was carefully selected to optimize imaging penetration and resolution, ensuring clear visualization of delicate retinal structures during complex therapeutic interventions. By integrating precise image guidance directly into the injection process, we aim to enhance the accuracy, safety, and potential effectiveness of emerging vision restoration techniques.

Text: Karol Karnowski, PhD, Acting IDoc Leader

Project team:

Karol Karnowski

Wiktor Kulesza

Jadwiga Milkiewicz

Piotr Nalewajko

Project in collaboration with other ICTER’s POB and OBi groups.

Related funding: IRAP (MAB) FENG by FNP

Reference:

  1. Piotr Węgrzyn, Wiktor Kulesza, Maciej Wielgo, Sławomir Tomczewski, Anna Galińska, Bartłomiej Bałamut, Katarzyna Kordecka, Onur Cetinkaya, Andrzej Foik, Robert J. Zawadzki, Dawid Borycki, Maciej Wojtkowski, and Andrea Curatolo “In vivo volumetric analysis of retinal vascular hemodynamics in mice with spatio-temporal optical coherence tomography,” Neurophotonics 11(4), 045003 (8 October 2024). https://doi.org/10.1117/1.NPh.11.4.045003
16.12.2024

Surgery guidance and therapy administration

In this project, we address two primary challenges in ophthalmic surgeries: enhancing the accuracy and precision of surgical procedures and developing targeted drug and therapy administration methods for specific eye regions. To achieve these goals, we have developed an integrated image-guided and robotic-aided ocular microscopy platform that leverages Optical Coherence Tomography (OCT) image-guidance to improve surgical accuracy.

Our approach employs a dual cross-scan technique, with one scan recorded along the tool and the other across to the tool’s tip. This method facilitates real-time previews of the surgical area, providing depth information that are more interpretable than commonly used 3D visualizations. The 2D imaging approach offers additional advantages, being less computationally demanding and presenting potential for future cost-effective solutions.

The robotic arm, with a surgical tool mounted at the wrist, serves as a critical component of our system. It addresses several key aspects of ophthalmic surgeries: mitigating physiological tremors, supporting both surgeon assistance and fully automated operations, and providing instantaneous information about the tool’s tip position. This enables real-time locking of the OCT dual cross-scan pattern to the surgical tool position.

We are actively exploring various navigation information sources, including image-based methods from microscopes and OCT, as well as non-image-based approaches. Currently, our research focuses on developing novel retinal injection tools aimed at improving the effectiveness of vision restoration treatments.

Text: Karol Karnowski, PhD, Acting IDoc Leader

Project team:

Karol Karnowski

Krzysztof Gromada

Piotr Nalewajko

Adam Kurek

Tomasz Gawroński

Andrea Curatolo

Project in collaboration with other ICTER groups.

Related funding: IRAP (MAB) and IRAP (MAB) FENG – FNP

References:

1. Karol M. Karnowski, K. Gromada, T. Piesio, P. Ciąćka, A. Kurek, A. Curatolo „Real-Time OCT Cross-Section Display via Robotic Arm-Guided Surgical Tool,”, The Optica Biophotonics Congress: Biomedical Optic, Fort Lauderdale, USA, 09.04.2024, oral presentation

2. K. Karnowski, K. Gromada, T. Piesio, P. Ciąćka, A. Kurek, A. Curatolo, „Ophthalmic intraoperative OCT system with robotic arm-based tracking of surgical tools,” Photonics West, San Francisco, USA, 28.01.2024, oral presentation

3. K. Karnowski, K. Gromada, T. Piesio, P. Ciąćka, A. Kurek, A. Curatolo, „Robotic arm-based surgical tool tracking for real-time display of intraoperative OCT cross-sections at the surgical tool tip,” Microsimposium of the IPC PAS, 10.01.2024, oral presentation

4. K. Karnowski, K. Gromada, T. Piesio, P. Ciąćka, A. Kurek, A. Curatolo “Robotic arm-based surgical tool tracking for real-time display of intraoperative OCT cross-sections at the surgical tool tip,” The IRAP — Fostering Excellence and Innovation Conference, 12.10.2023, poster

5. K. Karnowski, K. Gromada, T. Piesio, P. Ciąćka, A. Kurek, A. Curatolo “Robotic arm-based surgical tool tracking for real-time display of intraoperative OCT cross-sections at the surgical tool tip,” Conference on Recent Advances in Translational Eye Research, 07.09.2023, poster

6. Karol Karnowski, “On imaging of structure and function

of the human cornea,” Conference on Recent Advances in Translational Eye Research, 08.09.2023, oral presentation

7. Karol Karnowski, Piotr Ciąćka, Andrea Curatolo, „Intraoperative ophthalmic OCT system tracking surgical tools at 200 Hz”, Photonics West, San Francisco, USA, 30.01.2023, oral presentation

15.12.2024

Development of new experimental approaches and computational tools for the analysis of single-cell sequencing data

Computational work in our lab focuses on developing new algorithms and scalable tools for analysis of massive single-cell datasets originated from wet lab and their integration across platforms and techniques. In particular, we are interested in creating new approaches for comprehensive inference of developmental trajectories and delineation of cell atlases from single-cell data, understanding the role of cell-to-cell signaling and biological pathways in lineage commitment and transitions between cellular states. We explore novel methods for multidimensional and multimodal data visualization to get comprehensive topography of the cellular landscapes. Single-cell multiomics sequencing will allow us to dissect the complex ecosystem of the tumour, the immune repertoire infiltrating it, and to understand the intercellular communication between immune subpopulations of cells. It will also provide new mechanistic insight into biology of cancer including uveal melanoma and point at the potential therapies.

15.12.2024

High-throughput single-cell sequencing in eye research (completed project)

Experimental part of the scientific activity of our group focuses mostly on leveraging high-throughput single-cell transcriptome and epigenome sequencing for interrogation of eye diseases, including retinal pathologies. Single-cell sequencing data enables to identify the previously unknown molecular mechanisms involved in inherited retinopathies and age-related eye diseases. Therefore, the perspectives of new therapies occur.

Team:

Dr. Marcin Tabaka

Dr. Damian Panas

Dr. Andrzej Foik

Dr. Jagoda Płaczkiewicz

Dr. Katarzyna Kordecka

Anna Galińska, MSc

References:

Leinonen H, Zhang J, Occelli LM, Seemab U, Choi EH, L P Marinho LF, Querubin J, Kolesnikov AV, Galinska A, Kordecka K, Hoang T, Lewandowski D, Lee TT, Einstein EE, Einstein DE, Dong Z, Kiser PD, Blackshaw S, Kefalov VJ, Tabaka M, Foik A, Petersen-Jones SM, Palczewski K. A combination treatment based on drug repurposing demonstrates mutation-agnostic efficacy in pre-clinical retinopathy models. Nat Commun. 2024 Jul 15;15(1):5943. doi: 10.1038/s41467-024-50033-5. PMID: 39009597; PMCID: PMC11251169.

Du SW, Komirisetty R, Lewandowski D, Choi EH, Panas D, Suh S, Tabaka M, Radu RA, Palczewski K.  Conditional deletion of miR-204 and miR-211 in murine retinal pigment epithelium results in retinal degeneration. J Biol Chem. 2024 Jun;300(6):107344. doi: 10.1016/j.jbc.2024.107344. Epub 2024 May 4. PMID: 38705389; PMCID: PMC11140208.

Engfer ZJ, Lewandowski D, Dong Z, Palczewska G, Zhang J, Kordecka K, Płaczkiewicz J, Panas D, Foik AT, Tabaka M, Palczewski K. Distinct mouse models of Stargardt disease display differences in pharmacological targeting of ceramides and inflammatory responses. Proc Natl Acad Sci U S A. 2023 Dec 12;120(50):e2314698120. doi: 10.1073/pnas.2314698120. Epub 2023 Dec 8. PMID: 38064509; PMCID: PMC10723050.

Luu JC, Saadane A, Leinonen H, Choi EH, Gao F, Lewandowski D, Halabi M, Sander CL, Wu A, Wang JM, Singh R, Gao S, Lessieur EM, Dong Z, Palczewska G, Mullins RF, Peachey NS, Kiser PD, Tabaka M, Kern TS, Palczewski K. Stress resilience-enhancing drugs preserve tissue structure and function in degenerating retina via phosphodiesterase inhibition. Proc Natl Acad Sci U S A. 2023 May 9;120(19):e2221045120. doi: 10.1073/pnas.2221045120. Epub 2023 May 1. PMID: 37126699; PMCID: PMC10175720.

Lewandowski D, Foik AT, Smidak R, Choi EH, Zhang J, Hoang T, Tworak A, Suh S, Leinonen H, Dong Z, Pinto AF, Tom E, Luu J, Lee J, Ma X, Bieberich E, Blackshaw S, Saghatelian A, Lyon DC, Skowronska-Krawczyk D, Tabaka M, Palczewski K. Inhibition of ceramide accumulation in AdipoR1-/- mice increases photoreceptor survival and improves vision. JCI Insight. 2022 Feb 22;7(4):e156301. doi: 10.1172/jci.insight.156301. PMID: 35015730; PMCID: PMC8876453.

Funds:

31.10.2023

IDoc Group achievements in 3 years perspective

One of the primary initiatives within the IDoc Group focuses on the development of safer and more effective tools for eye surgery. This endeavor posed a distinct challenge for us, as it fell outside our traditional areas of expertise. Nevertheless, it is indeed a remarkable achievement that we have managed to assemble a team that, in under three years, has successfully amalgamated diverse expertise and advanced the project to its current stage. Our journey was marked by a gradual accumulation of knowledge and experience, ultimately culminating in the integration of all the components.

We are now pleased to inform you of the initial experiments where a robotic manipulator has been deployed to enhance manual ophthalmic surgical procedures. These innovations are complemented by the integration of Optical Coherence Tomography (OCT) images, meticulously aligned with the surgical tools’ tip precise position.

Another project the IDoc laboratory has been involved in goes to the very core of what the ICTER research centre aims to develop, that is methods and instrumentation to detect proper eye structure and function and their alteration in case of disease in an objective way. We did so in collaboration with the POB lab, by pioneering a technique called optoretinography. We are combining this with structural biology tools from the ISB lab for analysing the cellular machinery and its complex changes during the visual cycle in order to validate our hypotheses about what process the functional signal we measure originates from. To do so we are validating our functional imaging results with electrophysiology methods together with OBi laboratory. 

It has been a challenging and ambitious project so far, but its collaborative nature made it all the more rewarding when not long ago we observed, in a repeatable way and for the first time, reduced functional responses from mice subject to temporal inhibition of vision, compared to their response only a couple of hours before the pharmacological treatment. We were able to objectively show with optoretinography that when a central protein (from the PDE family) involved in the phototransduction is inhibited, the mouse retinal photoreceptors, when exposed to a short flash of light, do not elongate nearly as much as they do when the mouse eye is fully functional. Measuring such a small physical change on photoreceptor length in vivo, as we are talking of only few tens of nanometers, can have a huge impact on vision science and ophthalmology by providing an objective functional test of visual ability and photoreceptor health. This in turns can speed up therapy selection and efficacy studies.

We look forward to upcoming results in this field.

Authors:

Dr. Karol Karnowski & Dr. Andrea Curatolo

28.08.2023

Diffuse optics and interferometry

Diffuse optics offers a noninvasive portable approach for examining biological tissues, including the human brain, in vivo [1]. Near-infrared spectroscopy (NIRS) [2] and diffuse correlation spectroscopy (DCS) are the primary diffuse optical modalities [3, 4]. In both approaches, the light illuminates the tissue, and diffusively scattered photons are collected at some distance from the emitter (typically 2-3 cm). NIRS uses the detected signal to estimate optical properties (absorption and scattering), while DCS quantifies the blood flow from temporal changes of the remitted light intensity. Although these methods have been applied to monitor brain oxygenation and blood flow, their most widely adopted versions rely on continuous wavelength (CW) lasers, precluding absolute measures of the optical and dynamical tissue properties [5].

Time-domain NIRS (TD-NIRS) enables quantification of the optical properties through the sample’s photon time-of-flight distribution (TOF distribution) [9-12]. This capability can also be combined with correlation spectroscopy to achieve TOF- (or photon path-length-) resolved blood flow information. So, we could better distinguish photons traversing superficial layers (short TOFs) from photons traveling deep into the brain (long TOFs). Also, given the TOF distribution, we could estimate the optical properties to achieve the absolute blood flow index (BFI), effectively combining the capabilities of TD-NIRS with DCS into a single modality. Such an approach is called time-domain diffuse correlation spectroscopy (TD-DCS) [6, 7].

Though TD-DCS is a powerful technique even applied in clinics, it relies only on light intensity. Therefore, TD-DCS does not enable the detection of the optical phase [8]. The optical phase is accessible in interferometric near-infrared spectroscopy (iNIRS) [9].

Interferometry in brain monitoring

Image: Interferometry in brain monitoring.

The optical phase is accessible in interferometric near-infrared spectroscopy (iNIRS). The iNIRS approach uses interferometry based on a temporally coherent tunable laser to achieve TOF resolution. Specifically, iNIRS supplements the conventional NIRS configuration with the tunable light source and the reference arm. The field remitted from the sample is recombined with the reference field. The beat frequency of the signal encodes photon path lengths (or times-of-flight). Short paths produce lower beat frequencies than long paths. Consequently, the photon time-of-flight distribution can be achieved by inverse-Fourier transforming the recorded signal. However, iNIRS provides much more information through the two-dimensional autocorrelation function (ACF) of the reemitted optical field. In iNIRS, the ACF is measured as a function of time lag with TOF resolution. This two-dimensional measurement (figure below) encodes information about the sample’s absorption, scattering, and blood flow index (BFI).

iNIRS was validated in in liquid phantoms [9], mouse brain [10], and human brain in vivo [11]. However, the original iNIRS (as DCS and TD-DCS) uses single-mode fibers for light collection, requiring integration times of 0.5-1 second. This time frame is too long, precluding the ability to detect rapid blood flow changes in the human brain that could be linked to neural signals.

To overcome those limitations, we recently proposed parallel interferometric near-infrared spectroscopy (πNIRS). In πNIRS we use multi-mode fibers for light collection and a high-speed, two-dimensional camera for light detection. Each camera pixel acts effectively as a single iNIRS channel. So, the processed signals from each pixel are spatially averaged to reduce the overall integration time. Moreover, interferometric detection provides us with the unique capability of accessing complex information (amplitude and phase) about the light remitted from the sample, which with more than 8000 parallel channels, enabled us to sense the cerebral blood flow with only a 10 msec integration time (∼100x faster than conventional iNIRS). We used such an approach to monitor the pulsatile blood flow in a human forearm in vivo. Also, we demonstrated that this approach could monitor the activation of the prefrontal cortex by recording the change in blood flow in the forehead of the subject while he was reading an unknown text [12].

Text: Dawid Borycki, PhD habil.

Team:

Dawid Borycki, PhD habil.

Michał Dąbrowski, PhD

Klaudia Nowacka, MEng

References:

  1. S. Samaei, P. Sawosz, M. Kacprzak, Z. Pastuszak, D. Borycki, and A. Liebert, “Time-domain diffuse correlation spectroscopy (TD-DCS) for noninvasive, depth-dependent blood flow quantification in human tissue in vivo,” Sci Rep 11, 1817 (2021).
  2. D. Borycki, O. Kholiqov, and V. J. Srinivasan, “Interferometric near-infrared spectroscopy directly quantifies optical field dynamics in turbid media,” Optica 3, 1471-1476 (2016).
  3. D. Borycki, O. Kholiqov, S. P. Chong, and V. J. Srinivasan, “Interferometric Near-Infrared Spectroscopy (iNIRS) for determination of optical and dynamical properties of turbid media,” Opt Express 24, 329-354 (2016).
  4. D. Borycki, O. Kholiqov, and V. J. Srinivasan, “Reflectance-mode interferometric near-infrared spectroscopy quantifies brain absorption, scattering, and blood flow index in vivo,” Opt Lett 42, 591-594 (2017).
  5. S. Samaei, K. Nowacka, A. Gerega, Z. Pastuszak, and D. Borycki, “Continuous-wave parallel interferometric near-infrared spectroscopy (CW piNIRS) with a fast two-dimensional camera,” Biomed Opt Express 13, 5753-5774 (2022).
16.08.2023

A new paper by IDoc group researchers, international scientists and a spin-off company published in “Biomedical Optics Express”

Whole-eye optical coherence tomography (OCT) imaging is a promising tool in ocular biometry for cataract surgery planning, glaucoma diagnostics and myopia progression studies. However, conventional OCT systems are set up to perform either anterior or posterior eye segment scans and cannot easily switch between the two scan configurations without adding or exchanging optical components to account for the refraction of the eye’s optics. In this work, we present the design, optimization and experimental validation of a reconfigurable and low-cost optical beam scanner based on three electro-tunable lenses, capable of non-mechanically controlling the beam position, angle and focus. The proposed beam scanner reduces the complexity and cost of other whole-eye scanners and is well suited for 2-D ocular biometry. Additionally, with the added versatility of seamless scan reconfiguration, its use can be easily expanded to other ophthalmic applications and beyond.

Text: Dr. Andrea Curatolo – Principal Investigator in the IDoc group at ICTER.

Publication:

María Pilar Urizar, Enrique Gambra, Alberto de Castro, Álvaro de la Peña, Onur Cetinkaya, Susana Marcos, and Andrea Curatolo, “Optical beam scanner with reconfigurable non-mechanical control of beam position, angle, and focus for low-cost whole-eye OCT imaging,” Biomed. Opt. Express 14, 4468-4484 (2023)

Link: https://opg.optica.org/boe/fulltext.cfm?uri=boe-14-9-4468&id=535917