Short Description

Displays a scale bar overlay on the sequence.
Warning: this plugin needs correct sequence metadata to be effective. Otherwise it will display wrong values.

Source code: https://gitlab.pasteur.fr/bia/scale-bar

Documentation

This plugin displays a scale bar overlay on the sequence in most 2D viewers, with the following options:

  • Location (choose from the four corners of the image or the viewer)
  • Color
  • Auto-adjust size: if ticked, scale bar size will adjust to changes in the units used for the pixel size in metadata and scale according to the size of the image
  • Size (manual)
  • Thickness
  • Display size: untick to show the bar only
  • Opacity

These options are accessible within the “Layers” section of the inspector (see screenshot below), and via the script editor:

importClass(Packages.plugins.tprovoost.scale.Scale)
Scale bar options

Important notes:

  • This plugin calculates the size of the scale bar based on the pixel size stored in the image metadata. Please make sure that the pixel size is correct, otherwise the scale bar will not be calibrated.
  • This plugin is a “startup” plugin, which means it runs in the background of Icy and will automatically add a scale bar on any opened sequence, as long as the plugin is “active”. Here are two ways to adjust its behaviour:
    • To hide the scale bar for a specific viewer, click on its “eye” icon on the “Layers” panel in the Inspector (see screenshot below).
    • To hide all scale bars and prevent scale bars from appearing automatically, the plugin can be deactivated from the “Preferences > Startup plugins” menu, by unticking “Enabled” and clicking on “Apply” or “Ok”.

      1. Click on Preferences
      2. Click on Startup Plugin
      3. Untick Enable and click on Apply
  • Note regarding screenshots: Icy’s screenshot feature will imprint all layers (including the scale bar) onto a final image that is then displayed in a new viewer. In theory, this new viewer containing the screenshot should also receive a scale bar of its own, which may be quite confusing for the user. Therefore, by default, screenshot viewers will automatically hide this extra scale bar (it can still be made visible by clicking on its “eye” icon in the layers panel).

    Left: By default, only the original scale bar, imprinted in the screenshot, is visible. Right: Displaying also the scale bar of the screen shot, with a different color and size to make it more visible.

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5 reviews on “Scale Bar”

  1. S
    I would like to be able to modify the scale bar and especially to remove text (eg. 10.0 um) from above it.
  2. l
    I also wish I could format the scale bar: color, length, thickness, and remove the text. I wish I could also fix the scale shown (for example 50uM), and the size of the bar would change with the zoom. Thanks a lot ! Laurent.
  4. IcyLyd
    February 2014 Very usefull but it would be great to chose the image we want to scale instead of scaling all pictures. The writing would be even smarter with white letters and black outline to stay away from the white square. IcyLyd Update November, 9th, 2014 Changing the size and the color is very suitable when using different fluorescent colored pictures. The fact that the scale bar is now following the picture instead of the viewer is very cool and avoid exporting picture without scale. Thanks for this update!
  5. A
    Ashwak Alshehri
    It's a good tool but I do have a few suggestions to make it more practical, so that I can use it in my results. 1- The option to remove text. 2-The option to change colours, scale bar thickness, and position (within a certain corner). 3- In the montage view of a multichannel image, in which multiple images are displayed in a row, it would be great if the scale bar only shows up in the corner of the whole montage, instead of being repeated onto every channel in the montage.

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Changelog

  • Version 3.3.1.0 • Released on: 2022-09-15 12:30:00
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    Description:

    Again improved / fixed drawing position logic (cannot probably do much better now)

  • Version 3.3.0.0 • Released on: 2022-09-14 17:00:00
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    Description:

    - improved drawing position logic
    - added 'opaque' parameter

  • Version 3.2.0.0 • Released on: 2021-03-17 11:00:00
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    Description:

    - fixed autoscale with large images
    - tweaked scale bar display (added shadow)
    - better unit selection system

  • Version 3.1.5.0 • Released on: 2017-09-19 10:08:18
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    Description:

    Fix compatibility issue with Java 6

  • Version 3.1.4.0 • Released on: 2015-05-28 00:07:07
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    Description:

    Fixed an issue that was allowing the scale bar placed on the image to grow larger than the image size when zooming out

  • Version 3.1.3.1 • Released on: 2015-02-11 17:39:24
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    Description:

    Re-uploaded .jar file

  • Version 3.1.3.0 • Released on: 2015-02-11 17:35:52
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    Description:

    Updated to EzPlug v.3.8.2 (color chooser)

  • Version 3.1.2.0 • Released on: 2014-12-01 13:09:50
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    Description:

    Hide the scale bar from Icy screenshots by default

  • Version 3.1.1.0 • Released on: 2014-11-20 11:14:48
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    Description:

    Fixed an issue with causing the scale bar not to initialise properly when started from Icy's preference window.

  • Version 3.1.0.0 • Released on: 2014-11-16 15:13:32
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    Description:

    * Settings are saved and reloaded at startup
    * fixed CPU leak
    * Location can be set relative to the image or the viewer
    * Adjusted default font and size
    * Thickness can be adjusted

  • Version 3.0.0.0 • Released on: 2014-11-07 18:26:13
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    Description:

    The new scale bar has arrived!
    Here are the new features:
    * Position relative to the image instead of the viewer
    * Adjustable options: color, size (manual & automatic), location (image corners), text display
    * Options are accessible within the "Layers" section of the inspector, and via the script editor

  • Version 2.0.2.0 • Released on: 2014-09-12 10:00:14
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    Description:

    Removed memory leak issue.

  • Version 2.0.1.0 • Released on: 2014-02-28 15:04:07
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    Description:

    Now display correctly on every 2D canvas (not only the default one).

  • Version 2.0.0.0 • Released on: 2013-07-03 12:15:38
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    Description:

    * Bottom left now. This will make it avoid being invisible because of the zoom factor is displayed at the same time
    * the scale bar now fully works

  • Version 1.6.0.0 • Released on: 2013-07-03 12:02:48
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    Description:

    * Uses orders of magnitude instead of precise values.
    * size of scale bar never changes now: will always be : size of the canvas / 8.

  • Version 1.5.0.0 • Released on: 2013-06-26 16:52:26
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    Description:

    * Now only updates text while zooming, and change the size and value after the zoom

  • Version 1.4.0.0 • Released on: 2013-06-26 11:20:13
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    Description:

    * fixed bar location issue

  • Version 1.3.1.0 • Released on: 2013-06-17 15:18:23
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    Description:

    * removed debug information

  • Version 1.3.0.0 • Released on: 2013-06-17 15:17:46
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    Description:

    * now scales with images zoom

  • Version 1.2.0.0 • Released on: 2013-06-17 14:15:50
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    Description:

    * removed white rectangle
    * now shadow on text

  • Version 1.1.0.0 • Released on: 2013-01-11 16:30:30
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    Description:

    Updated to 1.3.0.0

  • Version 1.0.0.2 • Released on: 2012-10-22 17:10:43
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    Description:

    * corrected 3D issue.

  • Version 1.0.0.1 • Released on: 2012-07-03 09:23:11
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    Description:

    Corrected issue with compilation.

  • Version 1.0.0.0 • Released on: 2012-07-02 21:17:10
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    Description:

    Updated to Icy last version.

  • Version 0.0.1.0 • Released on: 2012-06-20 14:33:49
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