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Correlations between lignin content and structural robustness in plants revealed by X-ray ptychography
摘要： Lignin is a heterogeneous aromatic polymer responsible for cell wall stiffness and protection from pathogen attack. However, lignin represents a bottleneck to biomass degradation due to its recalcitrance related to the natural cell wall resistance to release sugars for fermentation or further processing. A biological approach involving genetics and molecular biology was used to disrupt lignin pathway synthesis and decrease lignin deposition. Here, we imaged three-dimensional fragments of the petioles of wild type and C4H lignin mutant Arabidopsis thaliana plants by synchrotron cryo-ptychography. the three-dimensional images revealed the heterogeneity of vessels, parenchyma, and fibre cell wall morphologies, highlighting the relation between disturbed lignin deposition and vessel implosion (cell collapsing and obstruction of water flow). We introduce a new parameter to accurately define cell implosion conditions in plants, and we demonstrate how cryo-ptychographic X-ray computed tomography (cryo-PXCT) provides new insights for plant imaging in three dimensions to understand physiological processes.
关键词： lignin,structural robustness,X-ray ptychography,cryo-PXCT,plants,Arabidopsis thaliana
更新于2025-09-23 15:19:57
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Correlative 3D x-ray fluorescence and ptychographic tomography of frozen-hydrated green algae
摘要： Accurate knowledge of elemental distributions within biological organisms is critical for understanding their cellular roles. The ability to couple this knowledge with overall cellular architecture in three dimensions (3D) deepens our understanding of cellular chemistry. Using a whole, frozen-hydrated Chlamydomonas reinhardtii cell as an example, we report the development of 3D correlative microscopy through a combination of simultaneous cryogenic x-ray ptychography and x-ray fluorescence microscopy. By taking advantage of a recently developed tomographic reconstruction algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE), we produce high-quality 3D maps of the unlabeled alga’s cellular ultrastructure and elemental distributions within the cell. We demonstrate GENFIRE’s ability to outperform conventional tomography algorithms and to further improve the reconstruction quality by refining the experimentally intended tomographic angles. As this method continues to advance with brighter coherent light sources and more efficient data handling, we expect correlative 3D x-ray fluorescence and ptychographic tomography to be a powerful tool for probing a wide range of frozen-hydrated biological specimens, ranging from small prokaryotes such as bacteria, algae, and parasites to large eukaryotes such as mammalian cells, with applications that include understanding cellular responses to environmental stimuli and cell-to-cell interactions.
关键词： GENFIRE,x-ray fluorescence microscopy,frozen-hydrated biological specimens,3D correlative microscopy,x-ray ptychography
更新于2025-09-10 09:29:36
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[IEEE 2018 New York Scientific Data Summit (NYSDS) - New York, NY, USA (2018.8.6-2018.8.8)] 2018 New York Scientific Data Summit (NYSDS) - High-Performance Multi-Mode Ptychography Reconstruction on Distributed GPUs
摘要： Ptychography is an emerging imaging technique that is able to provide wavelength-limited spatial resolution from specimen with extended lateral dimensions. As a scanning microscopy method, a typical two-dimensional image requires a number of data frames. As a diffraction-based imaging technique, the real-space image has to be recovered through iterative reconstruction algorithms. Due to these two inherent aspects, a ptychographic reconstruction is generally a computation-intensive and time-consuming process, which limits the throughput of this method. We report an accelerated version of the multi-mode difference map algorithm for ptychography reconstruction using multiple distributed GPUs. This approach leverages available scienti?c computing packages in Python, including mpi4py and PyCUDA, with the core computation functions implemented in CUDA C. We ?nd that interestingly even with MPI collective communications, the weak scaling in the number of GPU nodes can still remain nearly constant. Most importantly, for realistic diffraction measurements, we observe a speedup ranging from a factor of 10 to 103 depending on the data size, which reduces the reconstruction time remarkably from hours to typically about 1 minute and is thus critical for real-time data processing and visualization.
关键词： MPI,Python,CUDA,GPU,X-ray ptychography
更新于2025-09-10 09:29:36