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tutorial [2017/06/12 19:16]
kbertra2 [Step 3: 2D operations]
tutorial [2017/06/30 20:08] (current)
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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 ==== Reference-free alignment ====  ==== Reference-free alignment ==== 
   - Select the [[eyes:​logics:​Alignment|]] logic and apply settings shown below. Use your preprocessed particles (the output of [[eyes:​logics:​Normalization|]];​ see Step 2: Preprocessing) as your "input images."​ {{ ::​selection_031.png |}}    - Select the [[eyes:​logics:​Alignment|]] logic and apply settings shown below. Use your preprocessed particles (the output of [[eyes:​logics:​Normalization|]];​ see Step 2: Preprocessing) as your "input images."​ {{ ::​selection_031.png |}} 
-  - Again select the [[eyes:​logics:​Alignment|]] logic and set to mode = AppendAliInfos. Use the "​AliInfos"​ of the previous logic as the input for "Align Infos" and use the "​Output"​ of the [[eyes:​logics:​Normalization|]] logic //(see Step 2: Preprocessing)//​ as the input for "​Images."​ //The output of the final [[eyes:​logics:​Alignment|]] logic is your set of aligned particles.//​ (If this is your first round of classification,​ skip the next step and move to //​Iteration//​.)+  - Select another ​[[eyes:​logics:​Alignment|]] logic from the **Logics Panel** ​and set to mode = AppendAliInfos. Use the "​AliInfos" ​output ​of the previous logic as the input for "Align Infos" and use the "​Output"​ of the [[eyes:​logics:​Normalization|]] logic //(see Step 2: Preprocessing)//​ as the input for "​Images."​ //The output of the final [[eyes:​logics:​Alignment|]] logic is your set of aligned particles.//​ (If this is your first round of classification,​ skip the next step and move to //​Iteration//​.)
  
 ==== 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 =====
  
-  - //​Extractbymember://  +After evaluation of your dataset using alignments and classifications you may want to exclude particles contributing to less well defined classes in your dataset. To do so, you may first use the [[eyes:interactive:​extract|interactive Extract]] logic to select poorly defined class sums, or those showing artefacts like hole borders, ethane blobs, etc. and then the [[eyes:​logics:​extractbymember|ExtractByMember]] logic to exclude particles from your dataset that contribute to these bad class sums. 
-Extractbymember ​ + 
 ===== Step 5: 3D startup ===== ===== Step 5: 3D startup =====
  
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 ===== Step 6: Refinement ===== ===== Step 6: Refinement =====
  
-  - //3D Refinement//: Find the "​3DOperations"​ logic group in the **Logics Panel** and select [[eyes:​logics:​3DRefinement|]]. Apply the following settings: {{ ::​selection_032.png |}} +//This Step is currently under construction.//
- +
-  +
-FSC +
-Sharpening +