Part of the Oxford Instruments Group

Batch Pipeline for Image Processing

Welcome to the Imaris 9.3 Tutorial: Batch Pipeline for image processing only – setting up and viewing the results

In this tutorial my goal is to process multiple images from the experiment using the same settings.

Here, I want to Deconvolve all channels.

To start setting up a  new Batch Pipeline simply select New Batch icon. Batch Pipeline Creator consists two major steps: Batch Setup Step 1 – Image processing and Batch Setup Step 2 – Object Detection. You can either set up the batch built of those two steps or skip the one which you don’t need.

In this tutorial I will show you how to set up and save a Batch image processing pipeline and how to view the results.

In the Batch Setup Step 1 – Image processing there is an image processing pipeline on the left and image processing preview window in the center. Now you can choose an image processing function from a dropdown menu next to a selected channel. Here I want to deconvolve all channels, so I select deconvolution for the red channel and  set up the parameters.

This image was acquired using spinning disk confocal. In this example, majority of the acquisition parameters is automatically read from metadata,

I only select silicon oil from the immersion medium dropdown menu.

Please watch the dedicated Imaris ClearView Deconvolution tutorial to learn more about other options.  Once the parameters are set for the red channel, you can copy and paste settings to other channels. If needed, you can also  set up  additional  image processing steps for selected channels, but I will skip this step in this tutorial. The results are immediately visible in the preview window. If you are happy with the preview, press “Next” button on the bottom of the pipeline editor. This takes you to the  Batch Setup Step 2- Object detection, but as you only want to deconvolve your images, skip this step. Make sure that the default option "Batch stores processed image is ticked" and press “OK” button.

In the pop-up window, enter the name of a new Batch – Deconvolution Batch. Now we are back in Arena again. There’s a new green arrow thumbnail representing our newly created Batch pipeline. First of all I would like to show you that the protocol is written in the same folder that images and when you copy the folder to another location, Batch protocol will be there (Right Click, Show in Explorer).

Now I’ll focus on editing and execution Batch image processing pipeline. Highlight the Batch protocol thumbnail with single left mouse click – Batch protocol properties appear in the right panel. There I can quickly review the content of my Batch. To edit this pipeline, click on the pencil icon above. To modify the Batch pipeline within the wizard, select the purple wizard icon (Edit). This option will get you again into the editor where you can precisely modify the Image processing Batch protocol or even add object detection on top. If you simply want to remove one “Brick” – selected command for one channel, right click and remove a brick.

Once the protocol is ready, Right-click the Batch Thumbnail and select Run Batch or Run Batch including subgroups, if you have other child folders in the parent folder. Batch always processes all images in the folder.

Batch progress bar appears in the right panel. Once the job is completed, you see green ticks next to all image names. Now you can see that every thumbnail got an icon showing that it includes 2 images. In fact both images are saved on the drive: raw and processed, but for simplification, in Arena you can see one thumbnail. Double clicking on the thumbnail, by default opens the processed image. You can always revert the processed version to the previous or original version in Arena by using the restore points.

Category: Tutorial

Download as pdf