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Last modified by flenners on 2026-02-04 17:25
From version 4.1
edited by flenners
on 2021-12-17 14:14
Change comment: There is no comment for this version
To version 12.1
edited by flenners
on 2024-05-24 14:52
Change comment: There is no comment for this version

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19 19  
20 20  **HOLOTOMO DATA**
21 21  
22 -We are still in "friendly user operation" for this mode and the reconstruction pipeline is still work in progress.
22 +Hint: you have to perform the phase reconstruction of your projections first! This is usually done by beamline staff. Then you can continue:
23 23  
24 -Update soon ...
24 +Go to "Load" tab. Click on "Load normalized data" at the bottom of the page and select your phase reconstruced projections.
25 25  
26 -= {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
26 +The common path is: ///asap3/petra3/gpfs/p05/YEAR/data/BEAMTIMEID/processed/SCANNAME/reco_~#~#//
27 27  
28 +Click on one file and click open
29 +
30 +You do not need to load any additional dark images.
31 +
32 +Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps are still optional. (see below)
33 +
34 +In principle, you can directly proceed to the third tab "Reconstruction". 
35 +
28 28  \\
29 29  
38 += {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
39 +
40 +(Can be skipped for Holotomography)
41 +
30 30  Go to "Prep" tab.
31 31  
32 32  The following is usually required for reconstruction:
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65 65  
66 66  **Finding the correct center of rotation. **
67 67  
68 -First, you have to find the correct center of rotation. For this, a single slice is reconstructed with different centers of rotation.
80 +First, you have to find the correct center of rotation. For this, a single slice is reconstructed with different centers of rotation
69 69  
70 -**Rot center:** For the start, enter half of your image size (1024 for unbinned data, 512 for data with binning 2.)
82 +**~1. Rot center: **Defines the rotation center in pixel coordinates. For the start, enter half of your image size (1024 for unbinned data, 512 for data with binning 2.)
71 71  
72 -**Delta:** Range which is reconstructed. Good starting value is 50. For fine rot center, choose 10. 
84 +**2. Delta: **Range of pixels around the in step 1 given rot center for which the test slice is reconstructed. Good starting value is 50. For fine rot center, choose 10. 
73 73  
74 -**Stepsize:** Stepsize beween the different rotation centers. Good start value is 5 and 1 for fine rot center.
86 +**3. Stepsize:** Stepsize beween the different rotation centers. Good start value is 5 and 1 for fine rot center. (for example [ ... , 507, 512, 517, ... ] for a stepsize of 5)
75 75  
76 -Slice: Slice which will be reconstructed. You can also check different slices for checking the rotation center.
88 +**4. Slice:** Defines the pixel row which is used to reconstruct the test slice. Tip: Choose a region where you expect to see distinctive structures. (You can also check different slices for checking the rotation center.)
77 77  
90 +**5. Check rotation center: **Click on the "Check rotation center" button.** **In the preview window move the slider around until you find the positions with the least artifacts. Remember the position number and check the Spyder Console to get the new rot center coordinates in pixel.
91 +
92 +[[image:attach:image2022-11-14_14-4-49.png||thumbnail="true" height="250"]]
93 +
94 +in blue the coordinate of the center of rotation; in yellow the position number of the preview slider
95 +
96 +**6. Update and Repeat:** Replace the Rot Center (step 1) with the new found coordinate, lower the Delta (step 2) and Stepsize (step 3) and repeat the process until you are satisfied with the result.
97 +
78 78  \\
79 79  
100 +How does a good rotation center look like?
101 +
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134 +The ghosting effect on the edges is due to sample movement during the scan.
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80 80  **Reconstruction Parameters. **
81 81  
82 82  When you found the correct rotation center, you can continue with the reconstruction.
83 83  
84 -Enter the final roation center from the above step.
167 +Enter the final roation center from the above step.
85 85  
86 86  You can select different reconstruction algorithms and filters. Standard is gridrec and shepp.
87 87  
Confluence.Code.ConfluencePageClass[0]
Id
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1 -275758009
1 +361457350
URL
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1 -https://confluence.desy.de/spaces/P5I/pages/275758009/03a Reconstruction with Reco GUI
1 +https://confluence.desy.de/spaces/P5I/pages/361457350/03a Reconstruction with Reco GUI