| 1. |
- Dierks, Hanna, et al.
(författare)
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Optimization of phase contrast imaging with a nano-focus x-ray tube
- 2023
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Ingår i: Applied Optics. - 1559-128X. ; 62:20, s. 5502-5507
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Tidskriftsartikel (refereegranskat)abstract
- Propagation-based phase contrast imaging with a laboratory x-ray source is a valuable tool for studying samples that show only low absorption contrast, either because of low density, elemental composition, or small feature size. If a propagation distance between sample and detector is introduced and the illumination is sufficiently coherent, the phase shift in the sample will cause additional contrast around interfaces, known as edge enhancement fringes. The strength of this effect depends not only on sample parameters and energy but also on the experimental geometry, which can be optimized accordingly. Recently, x-ray lab sources using transmission targets have become available, which provide very small source sizes in the few hundred nanometer range. This allows the use of a high-magnification geometry with a very short source-sample distance, while still achieving sufficient spatial coherence at the sample position. Moreover, the high geometrical magnification makes it possible to use detectors with a larger pixel size without reducing the image resolution. Here, we explore the influence of magnification on the edge enhancement fringes in such a geometry. We find experimentally and theoretically that the fringes become maximal at a magnification that is independent of the total source-detector distance. This optimal magnification only depends on the source size, the steepness of the sample feature, and the detector resolution. A stronger influence of the sample feature on the optimal magnification compared to low-magnification geometries is observed.
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| 2. |
- Dreier, Till, et al.
(författare)
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A USB 3.0 readout system for Timepix3 detectors with on-board processing capabilities
- 2018
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Ingår i: Journal of Instrumentation. - 1748-0221. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Timepix3 is a high-speed hybrid pixel detector consisting of a 256 x 256 pixel matrix with a maximum data rate of up to 5.12 Gbps (80 MHit/s). The ASIC is equipped with eight data channels that are data driven and zero suppressed making it suitable for particle tracking and spectral imaging.In this paper, we present a USB 3.0-based programmable readout system with online preprocessing capabilities. USB 3.0 is present on all modern computers and can, under real-world conditions, achieve around 320MB/s, which allows up to 40 MHit/s of raw pixel data. With on-line processing, the proposed readout system is capable of achieving higher transfer rate (approaching Timepix4) since only relevant information rather than raw data will be transmitted. The system is based on an Opal Kelly development board with a Spartan 6 FPGA providing a USB 3.0 interface between FPGA and PC via an FX3 chip. It connects to a CERN T imepix 3 chipboard with standard VHDCI connector via a custom designed mezzanine card. The firmware is structured into blocks such as detector interface, USB interface and system control and an interface for data pre-processing. On the PC side, a Qt/C++ multi-platformsoftware library is implemented to control the readout system, providing access to detector functions and handling high-speed USB 3.0 streaming of data from the detector.We demonstrate equalisation, calibration and data acquisition using a Cadmium Telluride sensor and optimise imaging data using simultaneous ToT (Time-over-Threshold) and ToA (Timeof- Arrival) information. The presented readout system is capable of other on-line processing such as analysis and classification of nuclear particles with current or larger FPGAs.
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| 3. |
- Dreier, Till
(författare)
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High resolution laboratory x-ray tomography for biomedical research : From design to application
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Laboratory x-ray micro- and nano-tomography are emerging techniques in biomedical research. Through the use of phase-contrast, sufficient contrast can be achieved in soft tissue to support medical studies. With ongoing developments of x-ray sources and detectors, biomedical studies can increasingly be performed at the laboratory and do not necessary require synchrotron radiation. Particularly nano-focus x-ray sources offer new possibilities for the study of soft tissue. However, with increasing resolution, the complexity and stability requirements on laboratory systems advance as well. This thesis describes the design and implementation of two systems: a micro- CT and a nano-CT, which are used for biomedical imaging.To increase the resolution of the micro-CT, super-resolution imaging is adopted and evaluated for x-ray ima- ging, grating-based imaging and computed tomography utilising electromagnetic stepping of the x-ray source to acquire shifted low-resolution images to estimate a high-resolution image. The experiments have shown that super-resolution can significantly improve the resolution in 2D and 3D imaging, but also that upscaling during the reconstruction can be a viable approach in tomography, which does not require additional images.Element-specific information can be obtained by using photon counting detectors with energy-discriminating thresholds. By performing a material decomposition, a dataset can be split into multiple different materials. Tissue contains a variety of elements with absorption edges in the range of 4 – 11 keV, which can be identified by placing energy thresholds just below and above these edges, as we have demonstrated using human atherosclerotic plaques.An evaluation of radiopaque dyes as alternative contrast agent to identify vessels in lung tissue was performed using phase contrast micro-tomography. We showed that the dye solutions have a sufficiently low density to not cause any artefacts while still being able to separate them from the tissue and distinguish them from each other.Finally, the design and implementation of the nano-CT system is discussed. The system performance is assessed in 2D and 3D, achieving sub-micron resolution and satisfactory tissue contrast through phase contrast. Applica- tion examples are presented using lung tissue, a mouse heart, and freeze dried leaves.
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| 4. |
- Dreier, Till, et al.
(författare)
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Improved resolution in x-ray tomography by super-resolution
- 2021
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Ingår i: Applied Optics. - 2155-3165. ; 60:20, s. 5783-5794
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, super-resolution imaging is described and evaluated for x-ray tomography and is compared with standard tomography and upscaling during reconstruction. Blurring is minimized due to the negligible point spread of photon counting detectors and an electromagnetically movable micro-focus x-ray spot. Scans are acquired in high and lowmagnification geometry, where the latter is used to minimize penumbral blurring fromthe x-ray source. Sharpness and level ofdetail can be significantly increased in reconstructed slices to the point where the source size becomes the limiting factor. The achieved resolution of the different methods is quantified and compared using biological samples via the edge spread function, modulation transfer function, and Fourier ring correlation.
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| 5. |
- Dreier, Till, et al.
(författare)
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Radiopaque dyes allow vessel imaging in lung tissue using laboratory phase contrast micro-CT
- 2022
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Ingår i: Proceedings of SPIE - The International Society for Optical Engineering. - : SPIE. ; 12242
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Konferensbidrag (refereegranskat)abstract
- Phase contrast micro-CT is a powerful technique allowing imaging of soft tissue at synchrotrons or using lab- oratory sources. The use of contrast agents is a useful approach when imaging vascular structures. However, common x-ray contrast agents typically rely on heavy metals to increase absorption, which may affect the phase contrast and cause artifacts in the reconstructed volumes. Thus, utilizing an agent with lower attenuation similar to soft tissue is clearly advantageous. Here, we evaluated different colored radiopaque solutions (tissue marking dyes) which had been injected into the vascular system of bovine lung samples, prior to embedding in paraffin. Scans were performed using a micro-focus x-tube calibrated to 10 µm spot size at 70 kV and a photon counting detector with a silicon sensor and 75 µm pixels. The resulting volumes have a voxel size of (25 µm)3, limited by the size of the samples, but sufficient to resolve the vascular system. Experiments confirmed that sufficient perfusion of the vessels with the dyes could be achieved, and the different dyes could be clearly discerned in the reconstructed volumes without causing artifacts allowing to clearly identify features in the soft tissue. Further, the findings were confirmed by histology.Keywords:
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| 6. |
- Dreier, Till, et al.
(författare)
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Super-resolution X-ray imaging with hybrid pixel detectors using electromagnetic source stepping
- 2020
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Ingår i: Journal of Instrumentation. - 1748-0221. ; 15:3
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Tidskriftsartikel (refereegranskat)abstract
- With increasing demand for high-resolution X-ray images, the super-resolution method allows to estimate a single high-resolution image from several low-resolution images. Hybrid pixel detectors provide high-quality and low-resolution images, which makes them particularlywell suited for super-resolution. However, such detectors consist of a limited number of pixels at high cost. Applying super-resolution with hybrid pixel detectors shows that it is a viable method to obtain high-resolution images. The point-spread function of such detectors can be idealised to be 1 pixel, adding no blur into the image making such detectors the ideal choice for the application of super- resolution X-ray imaging. However, there are charge sharing effects between the pixels caused by the energy and impact position of incoming photons. Utilising an X-ray source, which allows magnetic stepping of the X-ray spot, several slightly shifted images can be obtained without requiring mechanical movements. Registering the shifts between individual images with sub-pixel precision allows to estimate a high-resolution image. With repeatable and equally spaced X-ray spot position patterns, sufficient information can be obtained with only a few images. In this paper, we present the application of super-resolution for X-ray imaging using a Pilatus 100K hybrid pixel detector from Dectris Ltd. and a prototype micro-focus X-ray source from Excillum AB. Moreover, we analyse the image quality for applications in X-ray radiography and tomography. Using a sufficient number of low-resolution images allows us to achieve an increase in resolution, without introducing significant blur or artefacts into the image. Here we quantify the effects on the quality of resulting super-resolution images using different methods of image interpolation, interpolation factors, shifts of the sample on the detector, and amount of low-resolution images.
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| 7. |
- Kalbfleisch, Sebastian, et al.
(författare)
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X-ray in-line holography and holotomography at the NanoMAX beamline
- 2022
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Ingår i: Journal of Synchrotron Radiation. - : International Union of Crystallography (IUCr). - 0909-0495 .- 1600-5775. ; 29, s. 224-229
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Tidskriftsartikel (refereegranskat)abstract
- Coherent X-ray imaging techniques, such as in-line holography, exploit the high brilliance provided by diffraction-limited storage rings to perform imaging sensitive to the electron density through contrast due to the phase shift, rather than conventional attenuation contrast. Thus, coherent X-ray imaging techniques enable high-sensitivity and low-dose imaging, especially for low-atomic-number (Z) chemical elements and materials with similar attenuation contrast. Here, the first implementation of in-line holography at the NanoMAX beamline is presented, which benefits from the exceptional focusing capabilities and the high brilliance provided by MAX IV, the first operational diffractionlimited storage ring up to approximately 300 eV. It is demonstrated that in-line holography at NanoMAX can provide 2D diffraction-limited images, where the achievable resolution is only limited by the 70 nm focal spot at 13 keV X-ray energy. Also, the 3D capabilities of this instrument are demonstrated by performing holotomography on a chalk sample at a mesoscale resolution of around 155 nm. It is foreseen that in-line holography will broaden the spectra of capabilities of MAX IV by providing fast 2D and 3D electron density images from mesoscale down to nanoscale resolution.
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| 8. |
- Oikonomou, Vasileios, et al.
(författare)
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Elucidating the Bulk Morphology of Cellulose-Based Conducting Aerogels with X-Ray Microtomography
- 2023
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Ingår i: Advanced Materials Technologies. - : WILEY. - 2365-709X. ; 8:23
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Tidskriftsartikel (refereegranskat)abstract
- Conducting cellulose composites are promising sustainable functional materials that have found application in energy devices, sensing and water purification. Herein, conducting aerogels are fabricated based on nanofibrillated cellulose and poly(3,4-ethylenedioxythiophene) polystyrene sulfonate, using the ice templating technique, and their bulk morphology is characterized with X-ray microtomography. The freezing method (−20 °C in a freezer vs liquid nitrogen) does not impact the mean porosity of the aerogels but the liquid-N2 aerogels have smaller pores. The integration of carbon fibers as addressing electrodes prior to freezing results in increased mean porosity and pore size in the liquid-N2 aerogels signifying that the carbon fibers alter the morphology of the aerogels when the freezing is fast. Spatially resolved porosity and pore size distributions also reveal that the liquid-N2 aerogels are more inhomogeneous. Independent of the freezing method, the aerogels have similar electrochemical properties. For aerogels without carbon fibers, freezer-aerogels have higher compression modulus and are less stable under cycling compression fatigue test. This can be explained by higher porosity with larger pores in the center of liquid-N2 aerogels and thinner pore walls. This work demonstrates that micro-CT is a powerful tool for characterizing the morphology of aerogels in a non-destructive and spatially resolved manner.
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| 9. |
- Oikonomou, Vasileios, et al.
(författare)
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eSoil : A low-power bioelectronic growth scaffold that enhances crop seedling growth
- 2024
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : NATL ACAD SCIENCES. - 0027-8424 .- 1091-6490. ; 121:2
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Tidskriftsartikel (refereegranskat)abstract
- Active hydroponic substrates that stimulate on demand the plant growth have not been demonstrated so far. Here, we developed the eSoil, a low-power bioelectronic growth scaffold that can provide electrical stimulation to the plants' root system and growth environment in hydroponics settings. eSoil's active material is an organic mixed ionic electronic conductor while its main structural component is cellulose, the most abundant biopolymer. We demonstrate that barley seedlings that are widely used for fodder grow within the eSoil with the root system integrated within its porous matrix. Simply by polarizing the eSoil, seedling growth is accelerated resulting in increase of dry weight on average by 50% after 15 d of growth. The effect is evident both on root and shoot development and occurs during the growth period after the stimulation. The stimulated plants reduce and assimilate NO-3more efficiently than controls, a finding that may have implications on minimizing fertilizer use. However, more studies are required to provide a mechanistic understanding of the physical and biological processes involved. eSoil opens the pathway for the development of active hydroponic scaffolds that may increase crop yield in a sustainable manner.
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| 10. |
- Rix, Kristian R., et al.
(författare)
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Super-resolution x-ray phase-contrast and dark-field imaging with a single 2D grating and electromagnetic source stepping
- 2019
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Ingår i: Physics in Medicine and Biology. - : IOP Publishing. - 1361-6560 .- 0031-9155. ; 64:16, s. 1-8
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Tidskriftsartikel (refereegranskat)abstract
- Here we report a method for increased resolution of single exposure three modality x-ray images using super-resolution. The three x-ray image modalities are absorption-, differential phase- contrast-, and dark-field-images. To create super-resolution, a non-mechanically movable micro- focus x-ray source is used. A series of almost identical x-ray projection images is obtained while the point source is translated in a two-dimensional grid pattern. The three image modalities are extracted from fourier space using spatial harmonic analysis, also known as the single-shot method. Using super-resolution on the low-resolution series of the three modalities separately results in high- resolution images for the modalities. This approach allows to compensate for the inherent loss in resolution caused by the single-shot method without increasing the need for stability or algorithms accounting for possible motion.
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| 11. |
- Sala, Simone, et al.
(författare)
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Dose-efficient multimodal microscopy of human tissue at a hard X-ray nanoprobe beamline
- 2022
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Ingår i: Journal of Synchrotron Radiation. - 1600-5775. ; 29:3
-
Tidskriftsartikel (refereegranskat)abstract
- X-ray fluorescence microscopy performed at nanofocusing synchrotron beamlines produces quantitative elemental distribution maps at unprecedented resolution (down to a few tens of nanometres), at the expense of relatively long measuring times and high absorbed doses. In this work, a method was implemented in which fast low-dose in-line holography was used to produce quantitative electron density maps at the mesoscale prior to nanoscale X-ray fluorescence acquisition. These maps ensure more efficient fluorescence scans and the reduction of the total absorbed dose, often relevant for radiation-sensitive (e.g. biological) samples. This multimodal microscopy approach was demonstrated on human sural nerve tissue. The two imaging modes provide complementary information at a comparable resolution, ultimately limited by the focal spot size. The experimental setup presented allows the user to swap between them in a flexible and reproducible fashion, as well as to easily adapt the scanning parameters during an experiment to fine-tune resolution and field of view.
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| 12. |
- Solem, Rasmus, et al.
(författare)
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Material Decomposition in Low-Energy Micro-CT Using a Dual-Threshold Photon Counting X-Ray Detector
- 2021
-
Ingår i: Frontiers in Physics. - : Frontiers Media SA. - 2296-424X. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Material decomposition in computed tomography is a method for differentiation and quantification of materials in a sample and it utilizes the energy dependence of the linear attenuation coefficient. In this study, a post-image reconstruction material decomposition method is constructed for a low-energy micro-CT setup using a photon counting x-ray detector. The low photon energy range (4–11 keV) allows for K-edge contrast separation of naturally occurring materials in organic tissue without the need of additional contrast agents. The decomposition method was verified using a phantom and its capability to decompose biomedical samples was evaluated with paraffin embedded human atherosclerotic plaques. Commonly, the necessary dual energy data for material decomposition is obtained by manipulating the emitted x-ray spectrum from the source. With the photon counting detector, this data was obtained by acquiring two energy window images on each side of the K-edge of one material in the sample. The samples were decomposed into three materials based on attenuation values in manually selected regions. The method shows a successful decomposition of the verification phantom and a distinct distribution of iron, calcium and paraffin in the atherosclerotic plaque samples. Though the decompositions are affected by beam hardening and ring artifacts, the method shows potential for spectral evaluation of biomedical samples.
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| 13. |
- Truong, My, et al.
(författare)
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Sub-micrometer morphology of human atherosclerotic plaque revealed by synchrotron radiation-based μCT—A comparison with histology
- 2022
-
Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 17:4, s. 1-18
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Tidskriftsartikel (refereegranskat)abstract
- Histology is a long standing and well-established gold standard for pathological characterizations. In recent years however, synchrotron radiation-based micro-computed tomography (SRμCT) has become a tool for extending the imaging of two-dimensional thin sections into three-dimensional imaging of tissue blocks, enabling so-called virtual histology with arbitrary clipping planes, volumetric rendering and automatic segmentation. In this study, we present a thorough characterization of human carotid plaques after endarterectomy of patients with stroke or transient ischemic attack (TIA), investigating several different pathologic structures using both SRμCT and histology. Phase-contrast SRμCT was performed with two different magnifications (voxel sizes 6.5 μm and 0.65 μm, respectively), and histology was performed with multiple different stainings (Alpha-actin, Glycophorin A, von Kossa, Movat, CD68). The 0.65 μm high-resolution SRμCT was performed on selected areas with plaque typical relevant morphology, identified on the 6.5 μm low-resolution SRμCT. The tomography datasets were reconstructed with additional 3D volume rendering and compared to histology. In total, nine different regions with typical pathologic structures were identified and imaged with high-resolution SRμCT. The results show many characteristics typical for advanced atherosclerotic plaques, clinically relevant, namely ruptures with thrombosis, neo-vascularization, inflammatory infiltrates in shoulder regions, lipid rich necrotic cores (LRNC), thin fibrous cap, calcifications, lumen irregularities, and changes in vessel wall structures such as the internal elastic membrane. This method’s non-destructive nature renders details of micro-structures with an excellent visual likeness to histology, with the additional strength of multiplanar and 3D visualization and the possibility of multiple re-scans.
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| 14. |
- van der Have, Oscar, et al.
(författare)
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Shunt-type plexiform lesions identified in the Sugen5416/Hypoxia rat model of pulmonary arterial hypertension using SPµCT
- 2022
-
Ingår i: The European respiratory journal. - : European Respiratory Society (ERS). - 1399-3003 .- 0903-1936. ; 59:6
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Tidskriftsartikel (refereegranskat)abstract
- We recently described four distinct types of plexiform lesions in human idiopathic and familial pulmonary arterial hypertension (PAH) [1], visualising the three-dimensional lesion structure using synchrotron-based phase-contrast micro-CT (SPµCT). Two types, 1 and 2, are shunt-type lesions that connect pulmonary arteries to the bronchial circulation: type 1 to the vasa vasorum, and type 2 to peribronchial vessels. Type 3 lesions are found peripherally in the lung as spherical structures abruptly terminating the distal pulmonary artery/arteriole, and type 4 are characterised by recanalization of an occluded artery/arteriole. Our observation of type 1 and type 2 lesions in PAH supports previous work which demonstrated intrapulmonary bronchopulmonary anastomoses (IBAs) connected to plexiform lesions in human PAH, suggesting that shunting of blood can occur within lesions in the setting of supra-systemic pulmonary arterial pressure [2]. Further hemodynamic studies of distinct subtypes of plexiform lesions have been hampered by the lack of available animal models with plexiform lesions representative of the full range of lesion types found in human disease. Plexiform lesions have previously been described in the Sugen5416/Hypoxia rat model of pulmonary hypertension when time until sacrifice following hypoxia is extended to 13–14 weeks. Initially plexiform lesions were identified within the lumen as well as outside the vessel as aneurysm-like lesions [3], and recently the latter type was shown to form in supernumerary arteries [4]. However, neither study observed plexiform lesions communicating with the bronchial circulation, possibly because of methodological limitations of the histological analysis.
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