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High resolution electron tomography and segmentation-by-modeling interpretation in Bsoft.

ABSTRACT: Bsoft offers many tools for the processing of tomographic tilt series and the interpretation of tomograms. Since I introduced tomography into Bsoft almost two decades ago, the field has advanced significantly, requiring refinement of old algorithms and development of new ones. The current direct detectors allow us to collect data more efficiently and with better quality, progressing towards automation. The goal is then to also automate alignment of tilt series and reconstruction. I added an estimation of the specimen thickness as well as fiducialless alignment, to augment the existing fiducial-based alignment. High-resolution work requires correction for the contrast transfer function, in tomography complicated by the tilted specimen. For this, I developed a method to generate a power spectrum using the whole micrograph, compensating for tilting. This is followed by routine determination of the contrast transfer function, and correction for it during reconstruction. The next steps involve interpretation of the tomogram, either by subtomogram averaging where possible, or by segmentation and modeling otherwise. Such interpretation actually constitutes the main time-consuming part of tomography and is less amenable to automation compared to the initial reconstruction.

SUBMITTER: Heymann JB

PROVIDER: S-EPMC7737767 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Computational resources for cryo-electron tomography in Bsoft.

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2024-05-21 | PXD036885 | Pride

High-resolution in situ structure determination by cryo-electron tomography and subtomogram averaging using emClarity.

Project description:Cryo-electron tomography and subtomogram averaging (STA) has developed rapidly in recent years. It provides structures of macromolecular complexes in situ and in cellular context at or below subnanometer resolution and has led to unprecedented insights into the inner working of molecular machines in their native environment, as well as their functional relevant conformations and spatial distribution within biological cells or tissues. Given the tremendous potential of cryo-electron tomography STA in in situ structural cell biology, we previously developed emClarity, a graphics processing unit-accelerated image-processing software that offers STA and classification of macromolecular complexes at high resolution. However, the workflow remains challenging, especially for newcomers to the field. In this protocol, we describe a detailed workflow, processing and parameters associated with each step, from initial tomography tilt-series data to the final 3D density map, with several features unique to emClarity. We use four different samples, including human immunodeficiency virus type 1 Gag assemblies, ribosome and apoferritin, to illustrate the procedure and results of STA and classification. Following the processing steps described in this protocol, along with a comprehensive tutorial and guidelines for troubleshooting and parameter optimization, one can obtain density maps up to 2.8 Å resolution from six tilt series by cryo-electron tomography STA.

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Interpretation of very low resolution X-ray electron-density maps using core objects.

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High-Resolution Swin Transformer for Automatic Medical Image Segmentation.

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High resolution computed tomography in asthma.

Project description:OBJECTIVES: High-resolution computed tomography (HRCT) can detect the structural abnormalities in asthma. This study attempts to correlate these abnormalities with clinical and pulmonary function test (PFT) data. METHODS: Consecutive stable asthma patients attending Mubarak Al Kabeer Hospital, Kuwait, were subjected to HRCT during a six month period from July 2004 to December 2004, after initial evaluation and PFT. RESULTS: Of the 28 cases, sixteen (57.1%) had moderate, 6 (21.4%) had mild and 6 (21.4%) had severe persistent asthma. Thirteen (46.4%) patients had asthma for 1 to 5 years and 12 (42.9%) were having asthma for >10 years. Bronchial wall thickening (57.1%), bronchiectasis (28.6%), mucoid impaction (17.9%), mosaic attenuation (10.7%), air trapping (78.6%) and plate like atelectasis (21.4%) were noted. Bronchial wall thickening (p=0.044) and bronchiectasis (p=0.063) were most prevalent in males. Ten (35.7%) patients exhibited mild, 9 (32.1%) had moderate and 3 (10.7%) had severe air trapping. The difference in Hounsfield units between expiratory and inspiratory slices (air trapping) when correlated with percent-predicted FEV1 in right upper (r=0.25; p=0.30), left upper (r=0.20; p=0.41), right mid (r=0.15; p=0.53), left mid (r=-0.04; p=0.60), right lower (r=0.04; p=0.86) and left lower zones (r=-0.13; p=0.58) showed no relation. The same when correlated as above with the percent predicted FEF 25-75 did not show any significant association. The presence of air trapping was compared with sex (p=0.640), nationality (p=1.000), disease duration (p=1.000) and severity of symptoms (p=0.581). CONCLUSION: Abnormal HRCT findings are common in asthma; however, air trapping when present was not related to the duration or severity of the illness or to the FEV1.

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