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.

This is what a 2D image containing ROIs looks like in the Image Viewer

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.

Applications supporting ROIs are listed on the “Job Submission” page and marked with a small ROI symbol in the lower right corner

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”

Analyze 2D images containing ROIs 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 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”

Analyze 2D images containing ROIs starting from the Image Viewer

Viewing the progress of your analysis

Upon submitting the analysis job, a small pop-up window appears notifying you that the analysis is in progress. Wait until the task is completed. This might take a while. You will get an email notification once the analysis job has been completed.

From the Image Library

While you are still waiting, you can easily view the progress of the analysis job in the “Jobs” column in the Image Library of your project. This way is convenient if you have submitted just a couple of images for analysis.

View the progress of submitted analysis jobs in the “Jobs” column

From the Image Analysis

If you have submitted a large number of images for analysis, an easier way to view the progress of your analysis is through the Analysis Jobs section:

  1. Navigate to the Image Analysis page on the left-hand sidebar

  2. Once at the Image Analysis page scroll down

  3. Find the Analysis Jobs section

  4. Click through the Finished, Active and Failed jobs tabs

View the progress of submitted analysis jobs in the “Analysis Jobs” section

Viewing your image analysis results

For more information, please check this page How to download your image data analysis results?

 

You have done great progress by learning how to analyze 2D images with our Prisma apps!

Help your team members to learn this as well with your newly acquired knowledge.


If you have any questions, please send us an email at support@ikosa.ai.


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