(Pre-version 11) Batch Processor

The Batch Processor in Aivia can apply a recipe (or recipes) to multiple images at the same time as well as convert multiple images simultaneously to the Aivia TIFF format. When batch applying a recipe or recipes, the same recipe parameters and settings are used for all the input images. Batch application of recipes is useful for analyzing large sets of images with similar experimental conditions and acquisition criteria. Processed images can be loaded into Aivia for examination.

Please see the documentation for the Pixel Classifier for information on how to batch apply pixel classifiers.

Interface

The Batch & Cloud Processor window includes the Batch Processor as well as Aivia Cloud. To launch the Batch & Cloud Processor window, go to Analysis > Batch & Cloud Processor.

The four (4) types of jobs that can be run from the Batch & Cloud Processor window can be selected along the top of the Create Job tab. The Recipe and Convert job types are considered batch processes, while the Training and Applying job types are Aivia Cloud operations. The interfaces for batch recipe application and batch image conversion are shown in the respective expandable panels below.

Recipe apply

Open

Image conversion

Open

Batch operations are applied to all images placed in the Raw Input section. You can specify the target location for the processed images using the Output Dir text field and/or the adjacent Browse button. To start a batch operation, click the Create button in the lower right corner of the window.

Running a batch process

Batch processes are run from the Batch & Cloud Processor window, which can be launched from the Analysis menu in Aivia.

Select processing mode

The processing mode can be selected along the top of the Create Job tab in the Batch & Cloud Processing window. There are two (2) batch processing modes: Recipe and Convert.

Within Recipe mode, there are two (2) options for specifying recipe settings: Recipe Apply and Template Apply. With the Recipe Apply option, the Batch Processor applies the selected recipe with the settings set in the Recipe Console to all input images. With the Template Apply option, the Batch Processor applies the recipe and settings used to generate a specified object group to all input images and calculates the same measurements as are calculated for the template object group for each set of results. You may string together multiple recipes to batch apply simultaneously using the Add Another Recipe button.

In Convert mode, the Batch Processor converts images into the high-performance Aivia TIFF format for fast 3D volume rendering.

Select input images

To assign input images, first set the current library folder by clicking on the Add Local Folder button, navigating to the folder containing the input images in the dialog that appears, and then clicking on Select Folder. The contents of the selected folder are displayed in the Local Library section.

Select the images you wish to process in the Local Library section, and then either drag and drop them into the Raw Input section or right-click on the selected files and choose the Assign as Raw Input option. Hold down the Shift or Ctrl key during selection to select multiple files. To select all files in the current library folder, press Ctrl + A.

You can remove input images by selecting the thumbnails you would like to remove in the Raw Input section, right-clicking on the selected thumbnails, and then choosing the Remove option.

Select output folder

You can specify the save location for the processed images by clicking on the Browse button to the right of the Output Dir text field, navigating to the desired output location in the dialog that appears, and then clicking on Select Folder.

Run batch process

To apply the specified batch process to all input images, click on the Create button. The processed results are saved to the specified output folder. You can track the progress in the Progress Queue tab of the Batch & Cloud Processor window.

Batch applying recipes

The Recipe mode allows you to apply one (1) or multiple recipes to multiple images at once. The same recipe parameters and settings are used for all input images for a batch recipe process. The general workflow for Recipe mode is as follows:

1. Enter the desired recipe parameters into the Recipe Console and/or apply desired recipe(s) in the main Aivia window. (This requires an image to be loaded into Aivia.)

   1. Generally, using the Recipe Console to adjust the recipe parameters prior to batch applying a recipe is preferred. Using the Recipe Console, you can generate previews of the results for an image to ensure you have the correct settings.

2. Select recipe(s) and/or template object group(s) to use for batch applying in the Batch & Cloud Processor window.

3. Add images to the Raw Input section.

4. Specify the output location. 

5. Click Create to apply the recipe(s) to all input images.

Each processed image is saved as an Aivia TIFF to the specified output location along with an Excel file containing measurements for the results.

A tutorial on how to batch apply a recipe to multiple images can be found on the How to batch apply recipes page.

Batch converting images

The Convert mode allows you to convert and save multiple images to the high performance Aivia TIFF format. Before beginning the conversion process, please make sure that you have sufficient storage space for the converted images. While the batch processor is running, you may continue to use Aivia normally.

For detailed instructions on how to use the batch image conversion mode, follow the tutorial on the How to batch convert images to Aivia TIFF page.