Comments from review, and a short post-reconstruction section telling…

… the user to save it

docs/user_guide/index.rst

@@ -34,7 +34,9 @@ Firstly, let's load our projections. Go to "File" then "Load" or alternatively u
 #. Open one of the images with the prefix "Tomo".
 #. All images with the prefix "Tomo" in the same directory will be loaded
 
-Mantid Imaging should at this stage search the directory for all the files with prefixes like "Flat" and "Dark" and put them in the correct category. If this is missed or simply stored in a different location, the above steps can be repeated to find and load these.
+Mantid Imaging will search the directory for all the files with prefixes like "Flat" and "Dark" and put them in the correct category.
+Another location that is checked is the parent directory - it will search for folders names "Flat" and "Dark" there, and use those images for each one, respectively.
+If they are missed or stored in a different location, the above steps can be repeated to find and load these.
 
 At this stage there is also the option to:
 
@@ -56,11 +58,12 @@ Operations
 
 Next let's take the sample we loaded and let's tidy it up with operations. To open the operations go to "Workflow" then "Operations".
 
-1. **Remove Outliers** will be the first operation we will apply. This has to be completed in 2 modes "Bright" and "Dark". We'll complete this for both modes with difference set to 1000 and median kernel set to size 3. Apply this to all stacks.
-   - The difference value is used to find outliers, and will have to be adjusted depending on the values in your data.
+1. **Remove Outliers** will be the first operation we will apply. This has to be completed in 2 modes "Bright" and "Dark". We'll complete this for both modes with difference set to 500 and median kernel set to size 3. Apply this to all stacks.
+   - The difference value is used to find outliers, and will have to be adjusted depending on the values in your data, and how aggressive you want the filter to be.
+   - Safe Apply is enabled by default and it will show a window containing the original data and the processed data. This allows us to see the result of the operation before applying it. Choose the new data to proceed.
 
 2. **Flat Fielding** As we only have one set of flat and dark images we will set the flat fielding method to "Only Before". With safe apply checked running this operation opens the following window:
-   - Safe Apply window showing before flat fielding on the left and after flat fielding on the right. Allowing us to see the result of the operation before applying it. Next select "Choose New Data" to apply operation.
+   - Safe Apply window showing before flat fielding on the left and after flat fielding on the right. Next select "Choose New Data" to apply operation.
 
 .. image:: ../_static/flat_fielding.png
    :alt: Flat fielding with Safe Apply option turned on
@@ -74,15 +77,20 @@ Next let's take the sample we loaded and let's tidy it up with operations. To op
    :align: center
    :width: 70%
 
-At this point we have a sample ready to reconstruct. Note operations such as a median filter could be used here, but in an effort to conserve grey value as accurately as possible it was avoided.
+At this point we have a sample ready to reconstruct. Note: operations such as a Median Filter could be used here, but in an effort to conserve grey value as accurately as possible it was avoided. To see the list of available operations go to the :ref:`Operations` help page.
 
 
 Reconstruction
 ##############
 
-To open the reconstruction window, go to "Workflow" then "Reconstruct". This should open onto the "COR and Tilt" tab. For the reconstruction we will be manually finding the COR and tilt values. The best way to do this is be to use the \textbf{COR Table}.
+To open the reconstruction window, go to "Workflow" then "Reconstruct". This should open onto the "COR and Tilt" tab. The reconstruction window provides 2 automatic methods COR/Tilt finding, read more about them here: :ref:`Center of Rotation`.
+
+For this reconstruction we will be manually finding the COR and tilt values. The best way to do this is to use the **COR Table**.
+
+1. First select a slice index close to the top of the sample by clicking on the projection image (the top left image from the 3 visible in the window), or dragging the yellow line.
+
+   - Alternatively you can use the Preview box at the bottom of the reconstruction window.
 
-1. First select a slice index close to the top of the sample using the Preview box at the bottom of the reconstruction window.
 2. Then press the "Add" button at the bottom of the screen. This should add your slice to the table.
 3. Press the "Refine" button whilst selecting this slice. This brings up the following window:
 
@@ -91,9 +99,10 @@ To open the reconstruction window, go to "Workflow" then "Reconstruct". This sho
    :alt: Loading screen
    :align: center
 
-4. Continue by selecting which window shows the most accurate depiction of the sample. Mantid Imaging will highlight the window it feels is best in green.
-5. Repeat for a slice at the bottom.
-6. After this the "Calculate COR/Tilt from slice COR table" will now be selectable. Feel free to repeat the process for intermediate slices before pressing this button.
+4. Continue by selecting which image shows the most accurate depiction of the sample. Mantid Imaging will highlight the image it feels is best in green. This can be innacurate for very noisy samples, but should be accurate for this dataset.
+5. Select another slice at the bottom of the sample, "Add" it to the table.  As soon as you add the 2nd slice it will perform a fit for the COR and tilt. This will not be accurate - select the newly added row and repeat the refine.
+6. Once you find a good COR and confirmed with "Finish", the fit should be automatically performed to the new COR you found.
+
 
 Now move to the "Reconstruct" tab. At this stage there should several different settings to use. For this sample use the following settings.
 
@@ -104,4 +113,9 @@ Now move to the "Reconstruct" tab. At this stage there should several different
 
 There are many filter options. Experiment with the filters by looking at the slice preview and the corresponding histogram next to it. Filters like "hann" will strongly filter out higher frequency components. In contrast "ram-lak" preserves these higher frequency components resulting in a visibly less smooth histogram.
 
-Then click "Reconstruct Volume" to complete the reconstruction.
+Then click "Reconstruct Volume" to complete the reconstruction. This should take about 5 minutes.
+
+Post-reconstruction
+###################
+
+Once the reconstruction is finished, the data will be automatically divided by the pixel size, so the resulting images will contain the attenuation values. At this point you can apply some post-processing operations (such as circular mask), or just save out the stack with File > Save (or CTRL+S), in order to visualise it as a 3D volume in another software.

docs/user_guide/operations/index.rst

@@ -1,3 +1,5 @@
+.. _Operations:
+
 Operations
 ==========