Skip to Content
Last modified by flenners on 2026-02-04 17:25
From version 5.1
edited by flenners
on 2022-09-16 09:16
Change comment: There is no comment for this version
To version 2.1
edited by flenners
on 2021-12-07 14:27
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -1,8 +1,6 @@
1 1  = {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data
2 2  \\ =
3 3  
4 -**TXM DATA**
5 -
6 6  Go to "Load' tab and select year, enter your beamtime ID (e.g. 11001234) and press "enter" on keyboard.
7 7  
8 8  Now, the list of your scans will be shown below under "folder". Below folders, there are darks with different exposure times.
... ... @@ -13,31 +13,15 @@
13 13  
14 14  Loading the data can take some time (usually several minutes). The GUI will be blocked during this time.
15 15  
16 -Continue with next step, "Preparation".
14 +Continue with next step, "Preparation"
17 17  
18 18  \\
19 19  
20 -**HOLOTOMO DATA**
21 -
22 -Hint: you have to perform the phase reconstruction of your projections first!
23 -
24 -Go to "Load" tab. Click on "Load normalized data" at the bottom of the page and select your phase reconstruced projections.
25 -
26 -The common path is: ///asap3/petra3/gpfs/p05/YEAR/data/BEAMTIMEID/processed/SCANNAME/reco_~#~#//
27 -
28 -You do not need to load any additional dark images.
29 -
30 -Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps are still optional. (see below)
31 -
32 -In principle, you can directly proceed to the third tab "Reconstruction". 
33 -
34 -\\
35 -
36 36  = {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
37 37  
38 38  \\
39 39  
40 -Go to "Prep" tab.
22 + Go to "Prep" tab.
41 41  
42 42  The following is usually required for reconstruction:
43 43  
... ... @@ -79,40 +79,10 @@
79 79  
80 80  **Rot center:** For the start, enter half of your image size (1024 for unbinned data, 512 for data with binning 2.)
81 81  
82 -**Delta:** Range which is reconstructed. Good starting value is 50. For fine rot center, choose 10. 
64 +Delta: Range 
83 83  
84 -**Stepsize:** Stepsize beween the different rotation centers. Good start value is 5 and 1 for fine rot center.
85 -
86 -Slice: Slice which will be reconstructed. You can also check different slices for checking the rotation center.
87 -
88 88  \\
89 89  
90 -**Reconstruction Parameters. **
91 -
92 -When you found the correct rotation center, you can continue with the reconstruction.
93 -
94 -Enter the final roation center from the above step.
95 -
96 -You can select different reconstruction algorithms and filters. Standard is gridrec and shepp.
97 -
98 -You can also add ring removal (can take very long!!!!)
99 -
100 -Mask: If you like a circular mask around your data, check this box.
101 -
102 -before the final reconstruction, you can reconstruct a test slice to check your reconstruction parameters. Enter the slice number you want to reconstruct and press " Reconstruct slice".
103 -
104 104  \\
105 105  
106 -When you are happy with your result, press "Reconstruct full stack".
107 -
108 - You can check the data in ImageJ, and if you are not happy, you can also reconstruct with different parameters/ rotation centers.
109 -
110 -When you are finished with one scan, please press the "clear all" button! This saves the log data you see on the right, so you can later check what you did. The data are also removed from the memory.
111 -
112 112  \\
113 -
114 -\\
115 -
116 -\\
117 -
118 -\\
Confluence.Code.ConfluencePageClass[0]
Id
... ... @@ -1,1 +1,1 @@
1 -275770572
1 +236815113
URL
... ... @@ -1,1 +1,1 @@
1 -https://confluence.desy.de/spaces/P5I/pages/275770572/03a Reconstruction with Reco GUI
1 +https://confluence.desy.de/spaces/P5I/pages/236815113/03a Reconstruction with Reco GUI