How to use the Recipe Console

The Recipe Console is the primary module for performing image analysis in Aivia. You can select a recipe to run and modify detection parameters to optimize the analysis outcome. You can also save the analysis parameters to the recipe and re-use them for future analyses.

Launch the Recipe Console

The Recipe Console should be displayed by default when you first launch Aivia. You can find the Recipe Console tab in the Analysis Panel.

Manage recipes

You can load, save, and delete a recipe or recipe settings using the toolbar to the right of the Recipe dropdown menu. 

Open

The available options for recipe management are described in the table below.

Name	Icon	Description
Save Recipe	Open	Saves the current recipe and settings to a file
Load Recipe		Loads a recipe from a file; you may only load recipes that are compatible with your configuration of Aivia
Delete Recipe		Removes the current recipe from the recipe list and the Recipe Console; this will not delete your recipe from its file
Reload Recipe		Reloads the current recipe back to its previously saved state
Restore Standard Recipes		Restores the standard recipes that come with your installation of Aivia and removes all other recipes from the Recipe Console; this does not delete recipes from their files
Save Recipe Settings		Saves the current recipe settings to an XML file
Load Recipe Settings		Loads recipe settings from an XML file

Select recipe

To select a recipe, click on the Recipe dropdown menu in the top left corner of the Recipe Console interface. The dropdown menu contains all the recipes that are pre-installed with your copy of Aivia as well as any additional recipes that you have saved to and/or loaded from files.

A full list of the recipes that are available in Aivia is shown on the right.

After you select a recipe, the main Recipe Console window refreshes to display the relevant recipe interface.

Adjust recipe settings

Select recipe presets

Each recipe comes with preset groups with four (4) options prominently displayed: Low, Medium, High, and Custom. The Low, Medium, and High buttons are pre-configured with gradated parameter values to help you get started. The last button is for Custom settings and is automatically activated when you make changes to the recipe parameters.

Each preset option is linked to one (1) or more recipe parameters. To show the parameters, click on the caret next to the preset group name. To collapse the parameters, click on the caret again.

Automatically estimate parameters

Automatic parameter estimation is available for some recipes in Aivia, for which the Automatic Parameter Selection icon is active in the recipe header (see figure below). Click on the Automatic Parameter Selection icon to populate the recipe interface with parameters that are projected to be reasonable for the image based on the image data in the processing region and the processing functions (switchable options) you have selected. 

Load recipe settings

If you have recipe analysis results that were previously generated in Aivia, you can replicate the analysis directly by loading the recipe settings from the generated object set or from a file.

Each recipe-generated object group has a Load Recipe Settings button in the Object Set Settings panel; clicking on the button loads the recipe parameters used for generating the object set into the Recipe Console. If regions of interest (ROIs) were used for generating the object set, the settings that were used for each ROI will be loaded into the respective ROIs. The ROIs that were used will also be selected, and the ROIs that were not used will be deselected.

To load recipe settings from a file, you will need to have saved recipe settings to an XML file. Click on the Load Recipe Settings icon in the Recipe Console toolbar to launch the File Open dialog, where you may select the XML file to load.

Adjust recipe parameters

When the recipe presets are expanded, you can adjust the individual parameters associated with each preset group. There are three (3) ways to specify the value of a recipe parameter:

1. Click and drag the parameter slider.

2. Type a number into the numeric textbox.

3. Click on the up or down button for the numeric textbox.

Generally, entering a value in the textbox is the most precise method for entering a specific value; you can then use the up and down buttons for fine adjustments.

Each parameter has a pre-defined range of valid values. You can find out about the value range by hovering the cursor over an individual parameter. If you input a value that is outside the range of valid values, Aivia will automatically set the value to either the minimum or maximum value in the range based on which value is closer to the input value.

You can revert the parameter value to its previously saved value by clicking on the Revert button to the right of the parameter textbox.

You can find an explanation of the recipe parameters in the corresponding recipe page or by clicking on the question mark (?) to the right of the parameter textbox.

Change processing function

Some recipes allow you to switch to alternate processing functions for certain stages of the recipes. These alternative processing functions are often associated with certain parameters in the recipe and are indicated by the Switch icon to the left of the parameter name. When you click on the icon, a pop-up menu appears, listing the available processing functions. The current function is indicated with a check mark next to the function name. Click on a different function to switch processing functions.

Certain recipes let you skip a processing function. When you choose to skip a processing function, the parameters that are associated with the skipped function are disabled. Disabled parameters are grayed out, and you cannot enter parameter values for them.

Run recipe analysis

Select input and output

You can show the input and output locations for recipes by clicking on the caret next to the Input and Output text near the top of recipe interface. Click on the dropdown menus to select the desired input channel and output object sets. By default, when you select a new recipe, the output is set to the <Create Object Group> option to create a new object group as output. However, if you have existing object groups of the same type on the image, you may choose to overwrite an existing object group. Overwriting an object group deletes all objects existing in the group and then adds new objects to the group. 

Some recipes provide you with the option to add or remove certain outputs. These options appear in the Output Options menu, which you may access be clicking on the cog icon on the right side of the Input and Output section. Some outputs that you may choose not to generate have checkboxes next to their names in the Output Options menu. Output types for which you may generate multiple sets within the same object group, such as vesicles for the 3D Cell Analysis - Meshes/Spots recipe, have plus (+) and minus (-) buttons that you may click to increase and decrease the number of sets to generate. 

For images that have more than one z-plane, you may preview and/or obtain recipe results for regions of interest (ROIs). A table of ROIs is located at the bottom of the Input and Output section when ROIs may be used. Click on the the caret in the top-left corner of the Regions Of Interest Table to expand the table, which has options for you to add, remove, select, and otherwise manage ROIs.

If your license allows deep learning, you may select a model to apply to the input channel(s) prior to recipe processing. When a deep learning model is specified in the Input and Output section, the model is applied to the specified input channel(s), and then the output image(s) from the deep learning model is/are fed into the selected recipe.

Use regions of interest

For images with multiple z-planes, you may select ROIs to process using the checkboxes in the Regions Of Interest Table (see figure below) in the Input and Output section of the Recipe Console; the topmost checkbox (de)selects all ROIs. If any ROIs are selected, recipe previews and results are generated only for the selected ROIs. Previews of recipe results for ROIs are generated using the recipe settings that are in the Recipe Console; however, if any recipe settings are stored in an ROI, those settings are used for that ROI when the recipe is applied. You may use different recipe settings for different ROIs when applying a recipe, but overlapping ROIs must have the same recipe settings.

If you have not created any ROIs, Aivia will automatically generate a box ROI in the center of the image; you may manipulate the size and position of this box ROI by selecting it in the Image Viewer and clicking and dragging the red circles/spheres or by setting its precise position and dimensions in the Regions Of Interest Table. Use the three (3) buttons along the bottom of the Regions Of Interest table to generate additional ROIs. Please see the Regions of Interest page for more information about using ROIs.

Use a deep learning model

If your license permits it, you may load a deep learning model to use as a pre-processing step for a recipe. When a deep learning model is specified in the Deep Learning Model box of the Input and Output section, the model is applied to the input channel(s) of the recipe, and then the results are fed into the recipe pipeline. 

Preview recipe results

You can preview intermediate recipe results for preset groups by clicking on the magnifying glass icons next to their names. When you click on a magnifying glass icon, the Recipe Console applies the recipe to the current image up to the specified preset group and shows the intermediate results.

Depending on the preset group previewed, you may see a channel, objects, or both. You can toggle the display of these previews, which have a (Preview) suffix, from the Channel Settings and Object Set Settings panels. 

Apply recipe

When you are satisfied with the parameter settings, you can apply the recipe by clicking on one of the apply options in the lower right corner of the Recipe Console. If you are applying the recipe on the image from the beginning, you will be presented with two (2) options:

1. Start applies the recipe to the full image sequence from the first image or time frame.

2. Step applies the recipe to a single time frame.

When you have started to apply a recipe, the processing status is indicated in the Recipe Console next to the apply buttons. Recipe results on the last processed frame are displayed in the Image Viewer. The recipe apply progress is indicated with a red bar above the processed frame in the T/Z bar. Furthermore, you can temporarily pause recipe apply by clicking on the now-enabled Pause button.

While recipe processing is paused, you can modify the recipe parameters in the Recipe Console. When you are ready to proceed, you will have three (3) apply options:

1. Restart restarts recipe apply to the full sequence from the beginning, removing any processed data.

2. Continue resumes recipe apply from the current frame.

3. Step applies the recipe to the next time frame.

When the recipe has been applied to the full image sequence, the status message "Processing Completed" will appear to the left of the apply buttons.

Measurements on the recipe results are generated asynchronously, and progress is indicated in the lower right corner of Aivia's window. If you have a large image containing lots of objects, measurement calculation may persist after the recipe has finished applying. You may continue to use Aivia as usual while measurements are being calculated; however, please note that measurement data may be incomplete and not appear in the Spreadsheet or Charts until all the measurements are calculated.

Save recipe

There are several ways of saving the changes you have made to a recipe.

Export recipe to a file

You can export the recipe as a .recipe file by going to File > Export > Recipe from the top menu or clicking on the Save Recipe icon in the Recipe Console toolbar to open the File Save dialog where you may save the recipe.

Save parameters to presets

You can save custom parameters into one (1) of the three (3) preset buttons. Right-click on the preset button you wish to save the parameter value(s) to and select the Save Current Settings option from the context menu.

Save recipe settings to a file

You can save the recipe settings to an XML file that can be loaded into Aivia by clicking on the Save Recipe Settings icon in the Recipe Console toolbar. This will save the recipe parameters as well as any changes made to the switchable operating procedures to a text file in XML format. 

The recipe settings used for generating an object set during recipe apply are saved with the object set when the image is saved.