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The Recipe Apply mode in the Batch processor allows you to apply an analysis recipe to multiple images and export the analysis results to Excel. Prior to apply the analysis recipe, you can load an image into Aivia and use the Recipe Console interface to adjust the recipe parameters to give you the best results.

Step-by-step guide

Before beginning the tutorial, pelase download the Nuclei Count Demo Image (NucleiCountDemo.zip). For this tutorial, we will be using the Nuclei Count recipe for batch apply. Please refer to the documentations

As of Aivia 11, most batch processing in Aivia is done through the Workflow Processor. The Workflow Processor has options for saving processed images, Excel-readable measurement files, channels, and object masks. While you can create a workflow with multiple analysis steps, including pixel classification, image enhancement, object classification, and more in the Workflow Processor, the step-by-step guide on this page only covers a basic recipe workflow.

On this page:

Table of Contents

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Step-by-step guide

Info
This tutorial uses automatic workflow creation from an object group, but workflows can also be manually defined or created from recent actions. Please see the Workflow Processor page for more details.

Before beginning the tutorial, please download the Nuclei Count Demo Images (NucleiCountDemo.zip). This tutorial uses the Nuclei Count recipe. Please refer to the documentation on the Nuclei Count recipe for more information about the recipe.

You can download the image directly here.

1. Unzip the demo file

, there

. There should be

5

five images total.

2. Load one of the images into Aivia.

3. In the Recipe Console, click on the Recipe selection dropdown menu and select the Nuclei Count recipe.

4. Set the recipe parameters as

follows:

Image RemovedYou can view the results on the loaded image by clicking the From beginning

shown below.

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5. Click the Start button or press the F4 key on your keyboard to apply the recipe

Go to the Tools menu and select Batch Processor; this will launch the Aivia Batch Processor dialog

By default, the batch processor will have the Recipe Apply mode selected; click on the Add Image button to launch the Open dialog

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In the Open dialog

.

6. In the Object Set Settings panel, right-click on the created object group and choose the Create Workflow option. This creates a workflow with the analysis steps that were taken to create the object group, which in this case was applying the Nuclei Count recipe with the parameters specified in Step 4. This also launches the Workflow Processor.

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7. In the Workflow Processor window, click the Add File(s) button, navigate to the folder containing the unzipped demo images

and select all the files to open in the Batch Processor

in the dialog that opens, select the five demo images, and then click Open.

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Info

The exclamation point and yellow border around the workflow tile indicate that the workflow has not been saved to a file. To save the workflow for future use, go to the Editor tab and click the Save icon in the upper-right corner of the workflow’s tile. You can also make other modifications to the workflow in the Editor tab, such as renaming the workflow, adding additional processing steps, or changing the recipe or recipe parameters. See the Workflow Processor page for more details.

8. Click on the Browse button to the right of the

Output folder

Save Folder text field, navigate to

select

the desired output location

; by default, the batch processor will output to the %AppData%\AiviaBatch\Data folder

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You can choose to export data to Excel after apply automatically by checking the checkbox for Export Measurements to Excel

When you are satisfied with the parameters, close Aivia and click Run All to start the batch recipe apply process

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When processing is completed, a notification dialog will pop up; click OK and close the Aivia batch processor

Open the results folder, the processed images are indicated with the _Processed suffix and the exported measurements (if enabled) are indicated with the _PrintToExcel suffix

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You can open the processed image in Aivia to view the analysis results; or open the data spreadsheet in Excel to view the data

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Panel

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, and then click Select Folder.

9. In the Additional Save Options section, check the boxes for the types of output files you would like to save. With the Save Field option, the processed images with their generated objects and measurements are saved as Aivia TIFF files.

10. Click Run Job(s) to start the workflow processing. The Queue tab of the Workflow Processor is automatically shown, displaying the job currently being processed as well as the queue of jobs waiting to be processed. Once the queue is empty, all jobs have been completed.

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11. After processing is done, there is a folder within the specified save folder with the data, time, and workflow name in the title, and within that folder there is a folder for each of the input images titled “Job [#]” by default. Each “Job [#]” folder contains all outputs for one of the input images.

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12. You can open the processed images (if the Save Field output option was used) in Aivia to view the analysis results. You may click on the Explore Results Active Tile (accessed from the search bar) to adjust the Aivia layout to one conducive to exploring analysis results.

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