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How to manage multichannel images?

How to manage multichannel images?

Owned by polina.vinogradova (Unlicensed), created
Last updated: Mar 20, 2023 by fanny.dobrenova (Unlicensed)
4 min read

Get the best view of your multichannel images with IKOSA.

Find out about the ways to view multichannel images, adjust individual channel intensity as well as edit settings for the whole project!

What to expect from this page?

What are multichannel images?

Multichannel images are composite images consisting of different color channels stacked on top of each other. Multichannel images belong to the category of multidimensional images since each color channel represents an additional layer of information added to the images.

Please note: Multichannel images are sometimes referred to as “multiplex” or “multiplexed images” by the scientific community. If you want to learn more about multiplex images, check our article on the topic.

The pixel values for each channel in the image depending on the wavelength of light detected by the microscope. Unlike in the case of RGB images, where original pixel values might be lost due to the merging of channels, in multichannel images, this information is preserved. Yet, multichannel images cannot be properly displayed with conventional image viewing software. You need professional software with multichannel functionality to view these types of images.

How to upload multichannel images in IKOSA?

Please check this article https://kmlvision.atlassian.net/l/cp/gHgtA11z

Viewing multichannel images in IKOSA

You can view multichannel images in IKOSA as one composite overlaid image or as individual channel images.

Please note: Multichannel images in the Image Library are marked with a small stack icon . The number next to this icon shows how many channels your image consists of.

Opening a multichannel image

To open a multichannel image in IKOSA follow the steps below:

  1. Select a Project from the Projects overview page

  2. Go to the Image Library

  3. Click an image of your choice to open it

  4. Click the Image Library page in the left-side menu to navigate between the images

Viewing multichannel setting

  1. Go to the Multichannel page in the left-side menu

  2. Here you can:

    1. Change the Linear/Logarithmic view of the histogram

    2. Show/hide channels

    3. Show/hide intensity ranges

Adjusting channel intensity

To ensure that your images have the right intensity for your analysis you can manually adjust these levels.

  1. Click the Channel Visualization button under the channels

  2. Navigate to a graph chart of the channel that you want to adjust

  3. Check the changes in the preview window

  4. Move the graph cursor to the desired position

  5. Click the Save and Apply button

Please note: depending on the way you want the intensity curve of the histograms to be positioned you can switch between linear and log views.

The linear view will plot the intensity curve by using equal spacings between the reference points. By enabling it the curve will help you access the distribution of the intensity values.

In case the curve is highly skewed in one direction, use log view. It will plot the intensity curve by scaling the reference points using percentage moves. The curve will appear more proportionally stretched across the chart.

Please note: by ticking or unticking the “Intensity scale sync.” checkbox you can change the appearance of all histograms at once.

Activated checkbox - all charts will be synchronized by the color channel layer with the highest intensity.

Deactivated checkbox - the curves will be stretched to maximum intensity value in the respective channel.

Editing multichannel settings

You can edit multichannel settings from the Image Viewer or Multichannel page itself.

Editing settings from the Image Viewer

  1. Go to Multichannel panel

  2. Click Edit multichannel settings button

  3. In the pop up window you can:

    1. edit current multichannel setting details and channel settings (if they are not default)

    2. change between the existing multichannel settings

    3. create new multichannel settings

Important: if you create new multichannel settings or change between the existing ones, at first don’t forget to “Apply Settings“ and already then to “Reload Viewer“.

Editing settings from the Multichannel page

  1. Go to Multichannel page on the left-side menu panel

  2. Here you can:

    1. edit current multichannel setting details and channel settings (if they are not default)

    2. change between the existing multichannel settings

    3. create new multichannel settings

Important: if you create new multichannel settings or change between the existing ones, don’t forget to “Apply Settings“.

Annotating multichannel images

Once in the Image Viewer, you can draw annotation shapes on your multichannel images. You can do this by selecting one of the drawing tools from the right-hand side toolbar.

If you draw your annotation shapes in one of the channel layers, it will appear respectively in all other channel layers of the image.

If you need help with annotations, please read our article https://kmlvision.atlassian.net/l/cp/ioNxeSnj

 

Now you are good to go and set up your first multichannel project in IKOSA.

If you found this tutorial helpful, share it with others on your social media channels!

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

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