How to analyze multichannel images?

Learn how to extract valuable data from your multichannel images.

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 multichannel images in IKOSA?

To perform a multichannel image analysis in IKOSA, you have to run an existing IKOSA application on images marked with the multichannel symbol. Before running a particular application, you need to make sure that it supports multichannel analysis. You can do this by accessing the Image Analysis Page from the main sidebar and viewing the list of Prisma Applications.

Check if a Prisma app supports multichannel images

Start the analysis from the Image Library

  1. Select a specific project in IKOSA

  2. Go to Image Library

  3. Select (a) multichannel image(s) marked with symbol

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

  5. Select a suitable IKOSA application supporting multichannel analysis (e.g. Sparkfinder)

  6. Define up to 5 channels for segmenting instances (e.g. cell nuclei) and up to 10 channels for biomarker/intensity analysis

  7. Additionally you can define regions framing instances and capture extra morphometric insights (e.g. Virtual Cytoplasm).

  8. Click “Start Job”

Analyzing multichannel images

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 IKOSA application supports ROI analysis and 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:

  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. Follow the steps described above.

Viewing the progress of your analysis

For more information, please check regarding section (see table of contents: Viewing the progress of your analysis) of this page How-to analyze 2D images?

Viewing your image analysis results

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


Please note: Sparkfinder is one of the apps for multichannel analysis. You can view detailed input settings and sample output results here


Now you are perfectly fit to perform your first multichannel analysis in IKOSA!

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