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:
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
Select a specific project in IKOSA
Go to Image Library
Select (an) image(s) for analysis
Click the image analysis button on the top-right menu in the Image Library
Select the IKOSA application you want to use
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.
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:
Click an image to open it in the IKOSA Image Viewer
Click the image analysis button at the bottom of the right-hand toolbar
Select the IKOSA application you want to use
Click “Start Job”
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
Select a specific project in IKOSA
Go to Image Library
Select (an) image(s) containing ROIs for analysis
Click the analysis button on the top-right menu in the Image Library
Tick the “Analyze ROIs” checkbox at the top of the pop-up window
Select the IKOSA application that supports region-of-interest analysis
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:
Click an image containing an ROI to open it in the Image Viewer
Click the image analysis button at the bottom of the right-hand sidebar
Tick the “Analyze ROIs” checkbox at the top of the pop-up window
Select the IKOSA application that supports region-of-interest analysis
Click “Start Job”