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tutorial [2017/06/12 20:11] kbertra2 [Step 4: Dataset cleaning] |
tutorial [2017/06/30 20:08] kbertra2 [Step 2: Preprocessing] |
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To start a project you first need to import your data. The [[eyes:logics:Import|]] logic loads your data into the Cow. | To start a project you first need to import your data. The [[eyes:logics:Import|]] logic loads your data into the Cow. | ||
- | - //Import:// Find the Logic Group entitled **BasicFunctions.** Click and drag the [[eyes:logics:Import|]] logic into your workspace. Click on the logic in your workspace and specify the properties of your data with the **Properties** window. For this tutorial, use the following settings: Dimensionality = 0, Number of images to read = 0, File type = Autodetect, File(s)/folder to import = (specify location of your data), Pixel size in Angstrom = (varies), Starting index = (varies). | + | - //Import:// Find the Logic Group entitled **BasicFunctions.** Click and drag the [[eyes:logics:Import|]] logic into your workspace. Click on the logic in your workspace and specify the properties of your data with the **Properties** window. For this tutorial, use the following settings: Dimensionality = Original, Number of images to read = 0, File type = Autodetect, File(s)/folder to import = (specify location of your data), Pixel size in Angstrom = (varies), Starting index = (varies). |
- Click the "Play" icon in your workspace to run the program. | - Click the "Play" icon in your workspace to run the program. | ||
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- //Coarsing:// Find the logic group **ImageOperations.** Click and drag the [[eyes:logics:BoxManipulation|]] logic into your workspace. In the **Properties** window, select "Coarse" and set the Coarse factor to 3. Connect the [[eyes:logics:BoxManipulation|]] logic to the [[eyes:logics:Import|]] logic. Note: if using multiple tabs in the GUI, simply click and drag the desired logic from the **History** window into the **Quick Access** window. Click the "Play" icon to run the new logic. {{ :selection_026.png |}} | - //Coarsing:// Find the logic group **ImageOperations.** Click and drag the [[eyes:logics:BoxManipulation|]] logic into your workspace. In the **Properties** window, select "Coarse" and set the Coarse factor to 3. Connect the [[eyes:logics:BoxManipulation|]] logic to the [[eyes:logics:Import|]] logic. Note: if using multiple tabs in the GUI, simply click and drag the desired logic from the **History** window into the **Quick Access** window. Click the "Play" icon to run the new logic. {{ :selection_026.png |}} | ||
+ | - //Filtering:// Find the logic group **ImageOperations.** Click and drag the [[eyes:logics:filtering|]] logic into your workspace. In the **Properties** window, apply the following settings: {{ ::selection_055.png |}} Connect the [[eyes:logics:filtering|]] logic with [[eyes:logics:BoxManipulation|]] of the previous step and click the "Play" icon to run the new logic. | ||
- //Normalization:// Select [[eyes:logics:Normalization|]] from **ImageOperations** In **Properties** apply the settings shown below. Connect with [[eyes:logics:Filtering|]] from the previous step and click "Play." //The output of [[eyes:logics:Normalization|]] is your set of preprocessed particles.// {{ :selection_029.png |}} | - //Normalization:// Select [[eyes:logics:Normalization|]] from **ImageOperations** In **Properties** apply the settings shown below. Connect with [[eyes:logics:Filtering|]] from the previous step and click "Play." //The output of [[eyes:logics:Normalization|]] is your set of preprocessed particles.// {{ :selection_029.png |}} | ||
===== Step 3: 2D operations ===== | ===== Step 3: 2D operations ===== | ||
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==== Alignment with reference ==== | ==== Alignment with reference ==== | ||
- | - Repeat steps 1-4 from **Generation of references** to generate another set of references. | + | - Repeat steps 1-4 from **Generation of references** to generate another set of references. Use the newest references each time but always use the original preprocessed particles. |
- Use new references (i.e. the output of each iterative [[eyes:logics:MassAlignment|]]) as the "Align Infos" for the [[eyes:logics:Alignment|]] logic. | - Use new references (i.e. the output of each iterative [[eyes:logics:MassAlignment|]]) as the "Align Infos" for the [[eyes:logics:Alignment|]] logic. | ||
- | - //Iteration:// Repeat steps 1- several times, but skip step 5 since a reference is created after each iteration. Use the newest references each time but always use the original preprocessed particles. | ||
===== Step 4: Dataset cleaning ===== | ===== Step 4: Dataset cleaning ===== | ||
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===== Step 6: Refinement ===== | ===== Step 6: Refinement ===== | ||
- | - //3D Refinement//: Find the "3DOperations" logic group in the **Logics Panel** and select 3DRefinement. Apply the following settings: {{ ::selection_032.png |}} | + | //This Step is currently under construction.// |
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- | FSC | + | |
- | Sharpening | + |