Aivia_AnalysisPanel.PNG
The Analysis Panel is located in the bottom right of Aivia. You can resize it vertically by using the blue dotted handle at the top middle, including hiding it by shrinking it all the way down. There are 4 modes in the Analysis panel: Recipe Console (default), Image Enhancement Tool, Charts, and the Neuron Editor. You can find out more about each of these tools by clicking the link for each one or looking below.



Recipe Console


Aivia_AnalysisPanel_RecipeConsole.PNGThe Recipe Console allows the user to run recipes, which are automated processing sequences. These sequences are designed to be mini-workflows in themselves. They take in an image channel and output various results such as another channel, surfaces or other objects. In this example we will look at the 3D Neuron Analysis recipe which takes in a single 3d timepoint for a neuron and gives 3D objects that represent the neuron such as a Soma, Dendrites and Spines. However, the ideas are generalized across all recipes.

At the top left is a drop-down menu where you can pick from the available recipes that are unlocked with your license. At the top right are the Save, Open, Remove Current, Reload Current and Clear All buttons. If you have made any changes to a recipe, you can save your changes to either the same file or a new one. By default, when you close Aivia it will remember what Recipes you have open, so if you save to a new file it will re-open that recipe again and list as available in the dropdown list.

The next part of the Recipe Console is the blue header for the currently opened recipe. On the right side is a toggle-all button that may be helpful to expand or collapse all of the subsections, explained next.

The main portion of the Recipe Console is different for various recipes, but for the one we are looking at it contains 4 subsections: Input and Output, Soma Detection, Dendrite Detection, and Spine Detection. Each of these sections can be expanded by clicking the little up-arrow on the left. The Input and Output section allows you to choose which channel will be processed by the recipe, and where the output should go.

Some recipes will allow for previews of a subsection. You will see a magnifying glass icon to the left of the arrow used to expand/collapse the subsection. Clicking it will generate and show you a preview, but keep in mind that the preview is only for that subsection. The final output will depend on that subsection, but can look vastly different from the preview generated.

Aivia_AnalysisPanel_RecipeConsole_DendriteDetection.PNGIf we expand the Dendrite Detection in our example, we see that along with the preset buttons for 'Small', 'Medium', and 'Large', we can set custom values for the available parameters. The best values to choose will depend on the data set and your use. The units will change based on the calibration you have set.

There is a green arrow/red arrow icon that appears on the left side of some recipes. It is an enable/disable icon for a part of the recipe.

There are X-arrow buttons on the far right of each changeable parameter, these will reset the value back to a default.

Aivia_AnalysisPanel_RecipeConsole_Bottom.PNGAt the very bottom of the Recipe Console are the control buttons. In left to right order we have Preview, From Beginning, Continue, and Step. If you change the parameters, you will need to run the recipe using the From Beginning button.
  • Preview does as you might expect. If it is possible for the recipe to give you a preview, this button will be clickable and it will show you a preview of the final output, but only for that t-frame or z-slice (depends on the recipe).
  • From Beginning will run the recipe from the beginning of the image. If you were in the middle, or had part or all of the recipe already run, it will do it all over.
  • Continue will run the recipe from the current t-frame. It is only available in some cases, and you should be viewing a frame adjacent to where the recipe was paused. When the recipe is running, the Continue button will become a Pause button. In this case the recipe will pause after finishing the current frame.
  • Step will run the recipe for the current frame only. You will be able to Step again, or hit Continue if you want to process more. You could also hit From Beginning if you want, although there is no advantage if you haven't adjusted the recipe's parameters.




Image Enhancement Tool


Image Enhancements are effectively recipes that are designed to improve your image in some way. The interface and how you use it is very similar to the Recipe Console. At the top is a drop-down menu that lets you select the enhancement / recipe you want to run. Below that is the header for the selected item with a toggle-button on the far right that toggles all the subsections below. Each of these subsections can be expanded by clicking the little up-arrow on the left. The Input and Output section allows you to choose which channel will be processed by the recipe, and where the output should go.

Aivia_AnalysisPanel_ImageEnhancement.PNGIn this example we only have one subsection with only one changeable parameter that we need to adjust. The input and output are ok, but we should adjust the Filter Size and use the Preview button (at the bottom left) to decide if we like the results.

Finally, pressing one of the apply buttons (bottom right) will run the filter and provide the result where we chose the output to go.
















Charts


The Charts Tab allows viewing of various charts. The Dot Plot, Trace Plot, Directional Plot, Lineage Plot, Flow Plot, Kymograph, and Object Histogram are available.
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Neuron Editor



The Neuron Editor is only available when you are in the 3D View. There are 5 Edit Modes: Dendrite Pencil, Connect Neurons, Delete Dendrite Points, Add Spines, and Add Soma.

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