Run recipe analysis
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.
Input and Output section (fully expanded) with the Output Options menu shown in the Recipe Console
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.
Options in the Regions Of Interest Table in the Recipe Console
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.