Web-based chilled electron microscope data analysis graphical system and method

A cryo-electron microscope and data analysis technology, applied in image analysis, image data processing, image enhancement, etc., can solve time-consuming and energy-consuming problems, achieve the effects of reducing manpower, increasing segmentation speed, and reducing memory consumption

Inactive Publication Date: 2019-11-22
南京信易达计算技术有限公司
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

At present, such segmentation is basically done manually, and the current popular cryo-electron microscope analysis software supports manual segmentation, but such manual segmentation is quite time-consuming and labor-intensive. In addition, it segments isosurface grids rather than 3D data volumes

Method used

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  • Web-based chilled electron microscope data analysis graphical system and method
  • Web-based chilled electron microscope data analysis graphical system and method
  • Web-based chilled electron microscope data analysis graphical system and method

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Experimental program
Comparison scheme
Effect test

Embodiment 1

[0035] A web-based graphical system for cryo-EM data analysis, such as figure 1 As shown, including visualization module 1, segmentation module 2 and matching module 3, such as image 3 As shown, the visualization module 1 includes volume rendering, isosurface and crystal model visualization, and the cryo-electron microscopy data includes density data and crystal data; the visualization module 1 is used for visualizing the reconstructed density data and crystal structure data, and the volume The drawing and isosurface are used to display the density data, and the crystal data is displayed by the crystal model visualization module; the crystal data is used to match the density data in the later stage to derive the structure of the density data; the segmentation module 2 is used to analyze the three-dimensional data volume of the density data according to The characteristics of the macromolecular structure are segmented; the matching module 3 is used to match the density data wi...

Embodiment 2

[0053] As the second embodiment of the present invention, the multi-objective fast marching method includes initialization and circulation, and the specific steps of initialization are:

[0054] (1) mark the point whose radius is r on the axis of symmetry as the active point, let its time value T(x, y, z)=0;

[0055] (2) Mark the 6-connected neighbors of the active point as a close set, T(x, y, z)=1 / F(x, y, z);

[0056] (3) Mark all other points as far points, T(x,y,z)=TIME_MAX.

[0057] The specific steps of the cycle are:

[0058] (1) If the close collection is empty, exit the loop. Otherwise, select the point (i, j, k) with the smallest arrival time in the close set;

[0059] (2) Determine whether this point (i, j, k) is an active point of other partitions, if so, delete point (i, j, k) from the close set, and return to the above step (1);

[0060] (3) mark the point (i, j, k) as the active point, and delete it from the close collection;

[0061] (4) Mark the neighbors...

Embodiment 3

[0065] As the third embodiment of the present invention, HBV and RHDV are automatically segmented by the traditional fast-forward method and the fast-forward method of the present invention, and the memory test is carried out, as shown in the following table:

[0066] data number of blocks Legacy Data Structure (MB) This embodiment data structure (MB) HBV 42 1208 410 RHDV 32 796 345

[0067] It can be seen from the table that the new data structure can greatly reduce memory consumption.

[0068] The visualization module in this web-based cryo-electron microscope data analysis graphical system and method can display the data content, can visually see the data content, segment the entire three-dimensional data body according to the characteristics of the polyhedron structure, and realize the multi-objective fast marching method. The global segmentation of molecules improves the segmentation speed and reduces manpower for biologists to quickly ...

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Abstract

The invention relates to the technical field of graphic processing, in particular to a web-based chilled electron microscope data analysis graphic system and method. The system comprises a visualization module, a segmentation module and a matching module. The visualization module comprises volume rendering, iso-surface and crystal model visualization, and chilled electron microscope data comprisesdensity data and crystal data. According to the invention, the visualization module can display data content; data content can be visually seen; the whole three-dimensional data volume is segmented according to the characteristics of a polyhedron structure, global segmentation of molecules is achieved through a multi-target fast marching method, the segmentation speed is increased, the situationthat virus structure characteristics are rapidly obtained for biologists through manpower is reduced, and memory consumption in an automatic segmentation algorithm is effectively reduced through a newdata structure; the multi-target fast marching method supports simultaneous segmentation of a multi-target region; the algorithm directly provides automatic selection of initial seed points; and a second step is added in the loop to ensure that each point is not segmented by a plurality of regions.

Description

technical field [0001] The invention relates to the technical field of graphics processing, in particular to a web-based cryo-electron microscope data analysis graphics system and method. Background technique [0002] Cryo-electron microscopy is an important means of studying the structure of biological macromolecules, and cryo-electron microscopy is an advanced cryo-electron microscopy instrument. It can instantly freeze biological samples to keep the tissue structure in a fresh state, and then use the electron microscope to take pictures. It is the only method that can study small to small proteins, protein complexes to organelles and even whole cells. Molecular weight The size spans 12 series. These unique properties make cryo-EM play an increasingly important role in structural biology. Biomacromolecules are composed of many small substructures. In order to understand its structure, it is an essential step in the analysis process to divide the whole macromolecule into ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06T7/11
CPCG06T2207/10012G06T2207/30004G06T7/11
Inventor 周会群王玲
Owner 南京信易达计算技术有限公司
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