Aivia Software
How to batch convert images to Aivia TIFF
- Hoyin Lai
- Aiden Maloney-Bertelli (Unlicensed)
- Won Yung Choi
As of Aivia 11, you can convert and save multiple images to the high performance Aivia TIFF format through the Workflow Processor. While the Workflow Processor runs, you may continue to use Aivia normally. The converted, saved files have the file extension .aivia.tif and contain a multi-resolution pyramid for fast volume rendering in Aivia.
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Step-by-step guide
Make sure you have sufficient storage space in the temporary cache folders and the output folder for the converted images before you start batch image conversion.
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 connection such as SATA, USB 3.1 or Thunderbolt 3.
1. Click Analysis > Workflow Processor or run the Workflow Processor command from the search bar to launch the Workflow Processor dialog.
2. Aivia comes with a basic image conversion workflow. To load it, click on the arrow on the right edge of the Load Workflow button and choose the Reload System Workflows option. A workflow called “Convert_To_Aivia_Format” should appear in the dialog.
3. If you are converting images made up of one file per image and do not need to add calibration during conversion, skip to step 8. Otherwise, click on the Editor tab in the right section of the Workflow Processor dialog.
4. Along the top of the Workflow Processor, click Format.
5. If you would like to calibrate the images when they are converted, check the Calibration box and enter the calibration information.
You may also specify calibration and make changes to calibration while viewing Aivia TIFFs in Aivia.
6. If you are converting image sequences (for example, importing a series of 2D z-frame images into a single 3D image), choose the Single from Many option. Otherwise, if you have one file per image, leave the Standalone Images option selected.
7. Once your formatting options have been chosen, click Run. This takes you to the Runner section of the Workflow Processor.
8. In the File Input section, click the Add File(s) button. Navigate to the files you would like to convert, select them, and then click Open.
9. In the Saving section of the Runner, click Browse, navigate to the desired output location, and then click Select Folder.
10. For the Additional Save Options, ensure Save Field is checked.
11. Click Run Job(s). The Workflow Processor will automatically display the Queue, where you can monitor which image is being converted and which images are still in line for conversion.
12. When processing has completed, 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 can load and view the images in 3D in less than five seconds.
Pre-version 11
The steps in this section are for batch converting in Aivia prior to version 11; however, slight variations of these steps can still be used in the latest Aivia and Aivia Community versions with the Deep Learning Processor and Batch Image Converter respectively in place of the Batch & Cloud Processor.
1. Go to the Analysis menu and select Batch & Cloud Processor; this launches the Batch & Cloud Processor dialog.
2. In the Create Job tab of the Batch & Cloud Processor, choose Convert mode.
3. Click on the Add Local Folder button, navigate to the folder containing the image files to convert in the dialog that opens, and then click on Select Folder.
4. Assign the images you would like to convert as input by either dragging them from the Local Library section and dropping them into the Raw Input section or by selecting them in the Local Library section, right-clicking on the selected thumbnail(s), and choosing the Assign as Raw Input option.
5. Repeat steps 3 and 4 to designate files for conversion that are in other folders, if applicable.
6. Click on the Browse button to the right of the Output Dir text field, navigate to the desired output location, and then click on Select Folder.
7. If you would like to calibrate the images when they are converted, check the Calibrate box and enter the calibration information.
8. Click Create to start the batch conversion process. You can monitor progress in the Progress Queue tab of the Batch & Cloud Processor window and continue to use Aivia normally while the batch process is running.
9. When processing has completed, 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 five (5) seconds.