Short Description

View your multi-channel data as a montage with one image per channel plus a merged, color channel (useful to create figures for communication)

Team: Bio Image Analysis Unit
Institution: Institut Pasteur
Website: https://icy.bioimageanalysis.org

Documentation

This viewer plugin will split all N channels of the active sequence into a montage of N+1 images, with one image for each channel, plus an additionnal color (merge) rendering.

Accessing the viewer

This viewer can be activated via the “viewing mode” drop-down list on any viewer, as shown below. If “channel montage” is not in this list, make sure it is installed (use the search bar, or the plugin browser)

How to access the

Using the viewer

The montage is currently assembled with the following rules:

  • Images are assembled automatically to fit best the shape of the window. This means that by resizing the window, you may switch a square-like montage (see screenshot below) to a linear horizontal (or vertical) montage, whichever you (or your favorite journal) fancy.
  • Images have a default maximum width or height of 250 pixels (whichever is bigger), separated by a 5-pixel margin. The size of these images can be adjusted using the dedicated option right above the views. The margin is currently fixed, but if you need more flexibility, feel free to send feedback via the forum!

And here is a list of features (and caveats) that you might otherwise figure out by yourself, it just saves you time:

  • Contrast: Images respect the colormap choices from the inspector. Therefore, you may continue adjusting the brightness/contrast using the blue and red bars to optimize the rendering
  • Grayscale: A grayscale checkbox lets you switch all single-channel views to grayscale, while only the final, merged image will remain colorized. This is particularly convenient when viewing low-contrast data, especially with a projector during a presentation, where you try to have people see something.
  • ROI: the regions of interest (ROI) are obviously the same in all views, and you can keep editing them in this viewing mode.
  • Screenshot issue: the two screenshot buttons on top of the viewer aren’t currently supported (they will be in the future). In order to get export nice renderings, you have to fall back to traditional screenshot programs (make sure the montage is big enough, those screenshots will have a low dpi resolution)

Here is a screenshot of the viewer, with the (default) colored view on the left-hand side, and the grayscale view on the right-hand side

Channel Montage screenshot

7 reviews on “Channel Montage

  1. Very helpful plugin! However, would it be possible to choose between having each channel in color or in grayscale (except overlay obviously)? This would be useful for color blind people or for presentation with poor contrast projectors! Thanks a lot :) UPDATE on oct 17: GREAT !!! The easiest way to make montage for figures!! Even better than what I expected! Many thanks :)
  2. Stephane Dallongeville
    Great plugin, nice integration in canvas system... Still it would be nice to have it supporting the "no ROI overlays" as the scale bar for instance. Same goes for the not yet implemented screen shot feature.
  3. IcyLyd
    It's great to save time with that plugin. Thanks. I'm looking forward the grid version ;o) IcyLyd Update on oct 16': I love the new shortcut under 2D, and the update of the size with the slidebar. Update on Feb 28': thansk for having nicely integrated the requested horizontal checkbox and the screenshot !
  4. The review author didn't let any comment.
  5. Great for montage! just one question is there a way to integrate a ROI as an inset?.. or with any other Icy plugin even before using the Channel montage?
  6. University of Birmingham
    Really useful! Thanks so much It would be great to have a feature that allows you to position where the merged colour image is - it defaults to the right of your single channels, but the convention in a lot of other software is to have the merge to the left... Small thing, but having that woudl make it easier to transition from other software to this Thank you!

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Changelog

  • Version 2.5.0.0 • Released on: 2020-04-08 19:15:00
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    Description:

    Tried to fix the transparent area which could contains garbage with screenshot action (Stephane).

  • Version 2.4.6.0 • Released on: 2016-12-11 15:49:27
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    Description:

    Fixed an issue caused when the image is not yet loaded when opening the viewer

  • Version 2.4.5.0 • Released on: 2015-07-30 18:04:47
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    Description:

    Fixed a bug causing the screenshot to fail on a movie

  • Version 2.4.4.0 • Released on: 2015-06-09 14:08:38
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    Description:

    * Upgraded to 1.6.1.1
    * Fixed a multi-threading issue

  • Version 2.4.3.0 • Released on: 2014-12-01 13:07:55
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    Description:

    Fixed the previous update (screenshot was cut along the Y axis)

  • Version 2.4.2.0 • Released on: 2014-12-01 12:51:34
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    Description:

    * Better solution to the (previous) alpha issue: no change, just cleaner
    * Adjusted screenshot to remove extra space outside the main view

  • Version 2.4.1.0 • Released on: 2014-11-27 11:08:32
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    Description:

    Fixed a display issue with 4-channel images

  • Version 2.4.0.0 • Released on: 2014-07-10 12:13:37
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    Description:

    Improved user interface to allow manual adjustment of both the image size and the margin

  • Version 2.3.1.0 • Released on: 2014-05-12 20:43:01
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    Description:

    Reduced memory footprint (should improve performance on 32 bit systems)

  • Version 2.3.0.0 • Released on: 2014-02-28 12:25:53
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    Description:

    * Added scrollbar to browse the view
    * Added support for the "remove channel" operation
    * New: possibility to lock the layout horizontally instead of rearranging the views within the available space.

  • Version 2.2.0.0 • Released on: 2013-11-12 15:21:44
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    Description:

    New: screenshot support (minimal)

  • Version 2.1.1.0 • Released on: 2013-10-16 17:52:09
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    Description:

    GUI enhancements (mouse wheel zoom, icons and labels)

  • Version 2.1.0.0 • Released on: 2013-10-16 14:43:15
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    Description:

    * Reworked canvas implementation (switched from heavy Canvas2D to lighter IcyCanvas2D)
    * ROI can now be edited with no constraint on the "Escape" key
    * Mouse image position is displayed
    * Toolbar is now in the viewer's toolbar

  • Version 2.0.0.0 • Released on: 2013-10-16 00:23:45
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    Description:

    * Plugin has now become a viewer (accessible from the viewer's drop-down list).
    * Improved figure placement
    * Support for grayscale views
    * Support for ROI editing

  • Version 1.0.0.0 • Released on: 2013-05-07 17:03:42
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    Description:

    Now uses the existing color maps and user adjusted contrast from the original viewer.

  • Version 0.0.1.0 • Released on: 2013-05-07 14:59:41
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