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Last modified by flenners on 2026-02-04 17:25
From version 1.1
edited by flenners
on 2021-12-07 13:37
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

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1 += {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data
2 +\\ =
3 +
4 +Go to "Load' tab and select year, enter your beamtime ID (e.g. 11001234) and press "enter" on keyboard.
5 +
6 +Now, the list of your scans will be shown below under "folder". Below folders, there are darks with different exposure times.
7 +
8 +Select the scan you want to reconstruct and choose the corresponding dark images.
9 +
10 +If you recorded your data after 2019, you can directly continue by clicking the "Load" button. This will read all data needed for reconstruction.
11 +
12 +Loading the data can take some time (usually several minutes). The GUI will be blocked during this time.
13 +
14 +Continue with next step, "Preparation"
15 +
16 +\\
17 +
18 += {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
19 +
20 +\\
21 +
22 + Go to "Prep" tab.
23 +
24 +The following is usually required for reconstruction:
25 +
26 +Click "Normalize" button. This will take several minutes.
27 +
28 +Click "Minus Log" button.
29 +
30 +Click "Rotate" button.
31 +
32 +\\
33 +
34 +The following steps are **optional:**
35 +
36 +**Cropping:** If your samples are significantly (% style="color: rgb(0,51,102);" %)__smaller__(%%) than the field of view, you can crop the data to reduce computation time and storage. Draw a rectangle around your sample by keeping the left mouse button pressed. Check that your sample stays inside that rectangle at all angles. If you are happy, press the "crop" button to crop your data.
37 +
38 +**Binning:** You can bin your data before reconstruction. Since the detector has a point spread function of 2-3 pixels, it is save to bin by a factor of 2 without loosing spatial resolution. This reduces computation time and storage space needed.
39 +
40 +**Padding:** If your samples are significantly __larger__ than the field of view, you can pad your data to prevent artifacts at the outer field of view. Example: 100
41 +
42 +**Filter Projections before reconstruction:** You can filter the data before reconstruction. This reduces the noise, but also can induce blurring in the data. Only recommended for very noisy data. Filtering after reconstruction is usually better.
43 +
44 +\\
45 +
46 +**Linogram alignment:** Linogram alignment if sample moved. Ask your local contact if this is necessary.
47 +
48 +\\
49 +
50 +**Save current stack.** Writes the normalized projections to your beamtime folder.
51 +
52 +\\
53 +
54 += {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
55 +
56 +\\
57 +
58 +**Finding the correct center of rotation. **
59 +
60 +First, you have to find the correct center of rotation. For this, a single slice is reconstructed with different centers of rotation.
61 +
62 +**Rot center:** For the start, enter half of your image size (1024 for unbinned data, 512 for data with binning 2.)
63 +
64 +Delta: Range 
65 +
66 +\\
67 +
68 +\\
69 +
70 +\\
Confluence.Code.ConfluencePageClass[0]
Id
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1 -236815077
1 +236815113
URL
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1 -https://confluence.desy.de/spaces/P5I/pages/236815077/03a Reconstruction with Reco GUI
1 +https://confluence.desy.de/spaces/P5I/pages/236815113/03a Reconstruction with Reco GUI