The Batch Processor in Aivia allows applying a recipe to multiple images at the same time. This option will apply the same recipe parameter settings across the selected images. The tool is useful for applying the analysis recipe to a large set of images with similar experimental conditions and acquisition criteria. The processed images can then be loaded into Aivia for examination.



Graphical User Interface


The graphical user interface (GUI) for the batch processor is shown below. You can toggle between different batch operation modes by clicking on the radio buttons at the top of the dialog. Batch operation is applied on all images that are added to the Images list found in the main area of the Batch Processor. You can specify the location of the processed images using the Output folder text field. To start the batch operation, click the Run All button in the lower right corner.

batchProcessor.png
Batch Processor GUI

Using the Batch Processor


The Batch Processor can be launched from the Tools menu in Aivia.

Select processor mode
There are two batch processor modes: Recipe Apply and Image Conversion. In the Recipe Apply mode, the batch processor applies the selected recipe with the specified setting on all added images. In the Image Conversion mode, the batch processor converts 3D volumetric images into the high-performance Aivia TIFF format for fast 3D volume rendering.

To select a batch process mode, click on the radio button next to the mode description at the top of the Batch Processor dialog. The available GUI options will update depending on the selected processing mode.

Add an image
To add an image to the Batch Processor, click on the Add Image button to launch the Open dialog. Once the Open dialog is launched, navigate to the location of the files you wish to process. You can select individual files and click the Open button to add them one-by-one or select multiple files at a time by holding down the Shift or Ctrl key on your keyboard during selection. To select all files in the folder, press Ctrl + A on your keyboard.

The selected images will be added to the Images list on the batch processor GUI.

Clear images

You can remove all images from the Images list by clicking on the Clear Images button to the right of the Add Image button. This will remove all selected images from the list.

Select output folder

You can specify the save location for the batch processed images by clicking on the Browse button to the right of the Output folder text field. This will open the Browse for Folder dialog which will allow you to navigate to the desired output location.

Note: Make sure the output location has sufficient disk space prior to starting the Batch Processor.

notificationDialog.PNG
Notification dialog

Apply batch process

To apply batch process to all added images, click on the Run All button. The processed results will be saved to the specified output folder location. You can track the progress of processing in the gray progress bar box to the left of the Run All button. A small notification dialog will pop-up when the batch processing operation is complete.


Batch apply recipe to images


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.

Tutorial

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 on the Nuclei Count recipe for more information about the recipe. You can download the image directly here.
  1. Unzip the demo file, there should be 5 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:
    • NucleiCountSettings.PNG
  5. You can view the results on the loaded image by clicking the From beginning button or press the F4 key on your keyboard to apply the recipe
  6. Go to the Tools menu and select Batch Processor; this will launch the Aivia Batch Processor dialog
  7. By default, the batch processor will have the Recipe Apply mode selected; click on the Add Image button to launch the Open dialog
    • batchProcessor_addImg.png
  8. In the Open dialog, navigate to the folder containing the unzipped demo images and select all the files to open in the Batch Processor
  9. Click on the Browse button to the right of the Output folder text field to select the desired output location; by default, the batch processor will output to the %AppData%\AiviaBatch\Data folder
    • batchProcessor_browse.png
  10. You can choose to export data to Excel after apply automatically by checking the checkbox for Export Measurements to Excel
  11. When you are satisfied with the parameters, close Aivia and click Run All to start the batch recipe apply process
    • batchProcessor_runAll.png
  12. When processing is completed, a notification dialog will pop up; click OK and close the Aivia batch processor
  13. 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
    • BatchOutputFolder.PNG
  14. You can open the processed image in Aivia to view the analysis results; or open the data spreadsheet in Excel to view the data
    • NucleiCount_Aivia.PNG

Batch convert images to Aivia TIFF


The Image Conversion mode in the batch processor 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 best file writing performance, we recommend storing the data files in a high-capacity solid state drive (SSD) connected by a high-bandwidth hardware connections such as SATA, USB 3.1 or Thunderbolt 3.

Tutorial

  1. Go to the Tools menu and select Batch Processor; this will launch the Aivia Batch Processor dialog
  2. In the Aivia Batch Processor dialog, select the Image Conversion option
  3. Click on the Add Image button to launch the Open dialog
  4. Navigate to the folder(s) where your original images are located and select the desired image file to convert
  5. Hold down the Ctrl or Shift key to select multiple files or press Ctrl + A on your keyboard to select all the image files you wish to convert; click Open to add the selected files
  6. Repeat the process for files in other folders you wish to convert
  7. Under the Output Folder option, click on the Browse button to launch the folder selection dialog
  8. Select the folder location where you wish to save the converted Aivia TIFF files and click OK.
  9. Click the Run All button to start the batch conversion process
  10. When processing is completed, a notification dialog will pop up; click OK and close the Aivia Batch Processor dialog
  11. You can find the converted Aivia TIFF files in the specified output folder; the files are now in Aivia's high performance TIFF format and you will be able to load and view the image in 3D in less than 5 seconds

Video