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eyes:logics:reconstruction [2017/06/09 16:44] vzinch |
eyes:logics:reconstruction [2017/06/12 17:33] (current) vzinch [Usage] |
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| ====== Reconstruction ====== | ====== Reconstruction ====== | ||
| - | THIS position should be used for a brief introduction (max 2 sentences!) of the logic, stating WHAT and WHY it is doing something. | + | This logic is needed to create a 3D structure from 2D projections with assigned Euler angles. |
| ===== Usage ===== | ===== Usage ===== | ||
| - | FIXME | + | Reconstruction in Fourier space generally takes less time than in Real space and the output is mostly the same quality. |
| - | Here, a general/generic description of HOW the logic is USED should be given. Try to be as general as possible, but also mention prerequisites, restrictions, advantages, requirements which are specific of this logic. Basically everything the user needs to know to successfully use this logic. | + | It is highly recommended to use 'Reproject 3D parameter', as comparison of output projections to input classes is the best way of estimating the quality of the generated 3D model. |
| ===== Modes===== | ===== Modes===== | ||
| ==== Fourier ==== | ==== Fourier ==== | ||
| - | Here, a short introduction for the given mode should be placed. Again, state WHAT and WHY this mode us useful in not more than 2 sentences. | + | This mode makes reconstruction in Fourier space and is generally faster than Real space reconstruction |
| |< 100% 30% >| | |< 100% 30% >| | ||
| ^ Parameters ^ Description ^ | ^ Parameters ^ Description ^ | ||
| | Pixel in Angstrom | Pixel size of the microscope | | | Pixel in Angstrom | Pixel size of the microscope | | ||
| - | | With gridding | FIXME | | + | | With gridding | Use [[http://cds.ismrm.org/ismrm-1999/PDF3/664.PDF|gridding reconstruction algorithm]] | |
| | Normalize 3D | Normalizes the obtained 3D structure (mean=0) | | | Normalize 3D | Normalizes the obtained 3D structure (mean=0) | | ||
| | → 3D normalization sigma | Sigma value for normalization | | | → 3D normalization sigma | Sigma value for normalization | | ||
| - | | Padding factor | ... descriptions | | + | | Padding factor | Factor by which the box is padded with zeroes in fourier space | |
| | Already phase flipped | Indicate whether phase flipping was applied on the previous steps | | | Already phase flipped | Indicate whether phase flipping was applied on the previous steps | | ||
| | Reproject 3D | Gives additional output of 2D reprojections of the obtained 3D structure | | | Reproject 3D | Gives additional output of 2D reprojections of the obtained 3D structure | | ||
| | Symmetry | Symmetry of the complex studied (if known) | | | Symmetry | Symmetry of the complex studied (if known) | | ||
| - | | With CTF | Indicate whether header files with CTF are available | | + | | With CTF | Indicate whether header values with CTF parameters are available | |
| |< 100% 30% >| | |< 100% 30% >| | ||
| ^ Input ^ Description ^ | ^ Input ^ Description ^ | ||
| | Input | Class averages with assigned angular info or alisums | | | Input | Class averages with assigned angular info or alisums | | ||
| - | | Pre 3D info | FIXME | | ||
| |< 100% 30% >| | |< 100% 30% >| | ||
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| ==== Real Space ==== | ==== Real Space ==== | ||
| - | Here, a short introduction for the given mode should be placed. Again, state WHAT and WHY this mode us useful in not more than 2 sentences. | + | This mode makes reconstruction in Real space |
| |< 100% 30% >| | |< 100% 30% >| | ||
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| ^ Input ^ Description ^ | ^ Input ^ Description ^ | ||
| | Input | Class averages with assigned angular info or alisums | | | Input | Class averages with assigned angular info or alisums | | ||
| - | | Pre 3D info | FIXME | | ||
| |< 100% 30% >| | |< 100% 30% >| | ||
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| ===== Concept ===== | ===== Concept ===== | ||
| - | In this paragraph, the "HOW a logic works under the hood" and WHY someone should use it can be elaborated with higher detail. Describes a scenario in an image processing workflow where this logic can be used to solve the resulting problem. Also, wikipages, publications or anything else describing the theory behind an algorithm should be linked here, if applicable. | + | Real Space mode uses the [[http://www.owlnet.rice.edu/~elec539/Projects97/cult/node2.html|Filtered Back-Projection]] method, but applies 2D filtering instead of 1D, that reduces sensitivity to noise. |
| + | Fourier Space Mode uses Fourier inversion method based on [[https://en.wikipedia.org/wiki/Projection-slice_theorem|central slice theorem]]. | ||
| + | More information about the reconstruction in Real and Fourier space can be found in Chapter 7 of the following [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3239172/pdf/cr100353t.pdf|review]]. | ||