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How to analyze 2D images?

How to analyze 2D images?

Speed up your image analysis workflows in IKOSA by learning how to handle 2D image analysis tasks.  

In bioimage analysis, you will be often confronted with 2D images. Unlike multidimensional images, 2D images do not contain any additional spatial or temporal dimensions.

In this article, we guide you through the processes of analyzing 2D images both containing and not containing regions of interest (ROIs).  

What to expect from this page?

Before the analysis

Before you start analyzing images, you need to complete a few steps:

  1. Create a project

  2. Upload images

How to analyze 2D images not containing ROI(s)?

To perform a 2D image analysis in IKOSA, you have to run an existing IKOSA application on images marked with the 2D symbol.

Start the analysis from the Image Library

  1. Select a specific project in IKOSA

  2. Go to Image Library

  3. Select (an) image(s) for analysis

  4. Click the image analysis button on the top-right menu in the Image Library

  5. Select the IKOSA application you want to use

  6. Click “Start Job”

Please note: You can select both images with and without ROIs for the analysis. ROIs will not be considered in this case and the entire images will be analyzed. ROIs will only be taken into account, if the “Analyze ROIs” option is checked when submitting the analysis job.

Analyze 2D images starting from the Image Library

Start the analysis from the Image Viewer

If you want to analyze a single image, you can start the analysis directly from the Image Viewer:

  1. Click an image to open it in the IKOSA Image Viewer

  2. Click the image analysis button at the bottom of the right-hand toolbar

  3. Select the IKOSA application you want to use

  4. Click “Start Job”

Analyze 2D images starting from the Image Viewer

How to analyze 2D images containing ROI(s)?

If you select images containing ROIs for the task, the analysis will be limited only to the selected regions in the image.

If you need to learn how to draw ROIs, check our article on this topic.

Before running a particular application, you need to make sure that it supports ROI analysis. You can do this by accessing the Image Analysis Page from the main sidebar and viewing the list of Prisma Applications.

Start the analysis from the Image Library

  1. Select a specific project in IKOSA

  2. Go to Image Library

  3. Select (an) image(s) containing ROIs for analysis

  4. Click the analysis button on the top-right menu in the Image Library

  5. Tick the “Analyze ROIs” checkbox at the top of the pop-up window

  6. Select the IKOSA application that supports region-of-interest analysis 

  7. Click “Start Job”

Start the analysis from the Image Viewer

If you want to analyze a single image, you can start the analysis directly from the Image Viewer:

  1. Click an image containing an ROI to open it in the Image Viewer

  2. Click the image analysis button at the bottom of the right-hand sidebar

  3. Tick the “Analyze ROIs” checkbox at the top of the pop-up window

  4. Select the IKOSA application that supports region-of-interest analysis  

  5. Click “Start Job”