Methods and systems for 3d structure estimation using non-uniform refinement

Abstract

There is provided systems and methods for generating 3D structure estimation of at least one target from a set of 2D Cryo-electron microscope particle images. The method includes: receiving the set of 2D particle images of the target from a Cryo-electron microscope; splitting the set of particle images into at least a first half-set and a second half-set; iteratively performing: determining local resolution estimation and local filtering on at least a first half-map associated with the first half-set and a second half-map associated with the second half-set; aligning 2D particles from each of the half-sets using at least one region of the associated half-map; for each of the half-maps, generating an updated half-map using the aligned 2D particles from the associated half-set; and generating a resultant 3D map using all the half-maps.

1 . A system for generating 3D structure estimation of at least one target from a set of 2D Cryo-electron microscope particle images the system comprising one or more processors and a data storage device, the one or more processors configured to execute:
 a particle image module to receive the set of 2D particle images of the target from a Cryo-electron microscope;   a reconstruction module to split the set of particle images into at least a first half-set and a second half-set, and to iteratively perform:
 determining local resolution estimation and local filtering on at least a first half-map associated with the first half-set and a second half-map associated with the second half-set; 
 aligning 2D particles from each of the half-sets using at least one region of the associated half-map; 
 for each of the half-maps, generating an updated half-map using the aligned 2D particles from the associated half-set; and 
 generating a resultant 3D map using the half-maps; and 
   an output module to output an estimated 3D structure of the target based on the resultant 3D map.   
     
     
         2 . The system of  claim 1 , wherein the local resolution estimation is determined using local windowed Fourier Shell Correlation (FSC) to separately measure the local resolution at a plurality of positions of the first half-map and the second half-map. 
     
     
         3 . The system of  claim 2 , wherein the local resolution estimation comprises:
 selecting successive subsections, each subsection having a centre position comprising one of the plurality of positions of the first half-map or the second half-map;   for each subsection, determining a resolution for the subsection using Gold-Standard FSC (GS-FSC) and associating the resolution with the centre position of the respective half-map; and   building a local resolution map comprising each of the centre positions and the associated resolution.   
     
     
         4 . The system of  claim 3 , wherein when the GS-FSC determination for a given subsection is below a predetermined threshold, the predetermined threshold becomes the resolution. 
     
     
         5 . The system of  claim 4 , wherein the local resolution estimation is repeated for multiple iterations, where each iteration comprises a different predetermined threshold, and wherein the local resolutions from each iteration for a given position are combined using a weighted sum weighted by the predetermined threshold used for that iteration. 
     
     
         6 . The system of  claim 4 , wherein the local resolution estimation is determined at spaced-apart positions on the first half-map and on the second half-map. 
     
     
         7 . The system of  claim 6 , wherein the local resolution estimation is determined with the space between positions at a first distance, and wherein at positions of higher resolution, local resolution estimation is determined with the space between positions at a second distance, the second distance is smaller than the first distance. 
     
     
         8 . The system of  claim 1 , wherein the local filtering comprises median filtering by replacing each local resolution estimation with a median of local resolution estimates within a predetermined distance. 
     
     
         9 . The system of  claim 1 , wherein the local filtering comprises local windowed Fourier-domain low-pass filtering. 
     
     
         10 . The system of  claim 1 , wherein the local filtering comprises local adaptive filtering. 
     
     
         11 . The system of  claim 10 , wherein the local adaptive filtering comprises Bessel-Lanczos filtering. 
     
     
         12 . The system of  claim 10 , wherein the local adaptive filtering comprises Gaussian kernel filtering. 
     
     
         13 . The system of  claim 1 , wherein performing local resolution estimation and performing local filtering can be collectively determined by performing optimization, the optimization comprising minimizing a discrepancy between the first half-map and the second half-map after each half-map is filtered by a parameterized filtering operation. 
     
     
         14 . The system of  claim 13 , wherein the filtering operation is selected from a group consisting of local adaptive filtering, neural network filtering, non-isotropic filtering, and masking. 
     
     
         15 . The system of  claim 13 , wherein minimizing the discrepancy comprises minimizing the squared distance between the locally filtered first map and the second map, added to the squared distance between the first map and the local filtered second map. 
     
     
         16 . The system of  claim 15 , wherein minimizing the discrepancy further comprises adding a smoothness penalty acting on the locally filtered first map and the locally filtered second map. 
     
     
         17 . The system of  claim 16 , wherein the smoothness penalty comprises a second-derivative operator. 
     
     
         18 . The system of  claim 1 , the reconstruction module further splits the first half-set into a first quarter-set and a second quarter-set and splitting the second half-set into a third quarter-set and a fourth quarter-set; and wherein the local resolution estimation and the local filtering are performed on quarter-maps associated with each quarter-set, the aligning performed on each of the quarter-maps, the updating performed on each of the quarter-maps, and the generating a resultant 3D map uses the updated quarter-maps. 
     
     
         19 . The system of  claim 18 , wherein performing local resolution estimation and performing local filtering can be collectively determined by performing optimization, the optimization comprising minimizing a discrepancy between the first quarter-set and the second quarter-set and between the third quarter-set and the fourth quarter-set, after each quarter-set is filtered by a parameterized filtering operation. 
     
     
         20 . The system of  claim 1 , wherein the local resolution estimation is determined using local windowed Fourier Shell Correlation (FSC), the local windowed FSC having a smooth window function and a tunable window size. 
     
     
         21 . The system of  claim 1 , wherein the local resolution estimation is determined by transforming local regions of the half-maps into a wavelet basis, and comparing signal and noise characteristics, in that basis, between the half-maps.