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This commit adjusts various colors to satisfy the checker. It also adds
theme-friendly preset color variables, and uses them where appropriate.
Co-authored-by: Claude Sonnet 4.5 <noreply@anthropic.com>
Copy file name to clipboardExpand all lines: _pages/editing/index.md
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@@ -85,23 +85,69 @@ allowing you to easily and cleanly modify text with italics, bold, ordered
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or bulleted lists, etc. This wiki, as a Jekyll site, uses
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[kramdown](https://kramdown.gettalong.org/syntax.html). A quick-reference can be found [here](https://kramdown.gettalong.org/quickref.html), and a general Jekyll support reference [here](https://www.markdownguide.org/tools/jekyll/). Also helpful is GitHub Flavored Markdown (GFM) guide found [here](https://guides.github.com/features/mastering-markdown/).
Note that the last example, colored text, is not really Markdown, but rather
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plain {% include wikipedia title="HTML" %}. However, Markdown does not have a
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syntax for changing text color, and it supports mixing in HTML, so you can use
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the technique above if you need text in different colors.
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### Colors
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Rather than hardcoding colors, it is better to use preset theme-sensitive color variables, as shown above. The following color presets achieve sufficient color contrast to meet accessibility standards:
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@@ -15,7 +15,7 @@ You have several options of how you can select your XML dataset file:
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- Use the file chooser (click **Browse ...**) to select the XML file
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- Type or copy & paste the full path of the XML file
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If the XML file was successfully recognized, the dialog will change and show a quick summary of the contents of the dataset (the number of views, attributes, etc...) in <spanstyle='color:green'>green</span>:
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If the XML file was successfully recognized, the dialog will change and show a quick summary of the contents of the dataset (the number of views, attributes, etc...) in <spanstyle='color:var(--fg-green)'>green</span>:
Copy file name to clipboardExpand all lines: _pages/plugins/flimj/index.md
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@@ -125,7 +125,7 @@ You may also change the "as" option to specify how the results are rendered. Cur
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-**Grayscale**: Linearly maps the middle 80 percentile of the result image's values to grayscale colors from black to white. Values below the 10th percentile and above the 90th percentile are rendered black and white respectively.
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-**Color**: Linearly maps the middle 80 percentile of the result image's values to colors from <spanstyle="color:hsl(20,100%,50%)">`hsl(20, 100%, 50%)`</span> to <spanstyle="color:hsl(220,100%,50%)">`hsl(220, 100%, 50%)`</span> (see color bar below). Out-of-range values follow the same rule as in **Grayscale**.
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-**Color**: Linearly maps the middle 80 percentile of the result image's values to colors from <spanstyle="color:var(--fg-red)">`hsl(20, 100%, 50%)`</span> to <spanstyle="color:var(--fg-blue)">`hsl(220, 100%, 50%)`</span> (see color bar below). Out-of-range values follow the same rule as in **Grayscale**.
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-**Composite Color**: Takes the color mapped to by **Color** but replace the brightness with the brightness of the intensity image (on the left of the **Preview** pane). This option makes the fitted image look more uniform by deemphasizing jittery low photon count pixels.
Copy file name to clipboardExpand all lines: _pages/plugins/interactive-marker-controlled-watershed.md
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@@ -60,8 +60,7 @@ In this plugin the markers are introduced interactively by the user using any of
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-**Merge labels**: merge together labels selected by either the **"freehand" selection too**l (on a single slice) **or the point tool** (on single or multiple slices). The zero-value label belongs to the watershed dams, therefore it will ignored in case of being selected. The first selected label value will be assigned to the rest of selected labels, which will share its color.
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<b><spanstyle="color:#f80000">Note</span></b>: to select labels on different slices, use the point selection tool and keep the SHIFT key pressed each time you click on a new label.
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{% include notice icon="note" content="To select labels on different slices, use the point selection tool and keep the SHIFT key pressed each time you click on a new label." %}
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-**Shuffle colors**: randomly re-assign colors to the labels. This is a very handy option whenever two adjacent labels present a similar color.
Copy file name to clipboardExpand all lines: _pages/plugins/morphological-segmentation.md
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-**Tolerance**: dynamic of intensity for the search of regional minima (in the extended-minima transform, which is the regional minima of the H-minima transform, value of h). Increasing the tolerance value reduces the number of segments in the final result, while decreasing its value produces more object splits.
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<b><spanstyle="color:#f80000">Note</span></b>: since the tolerance is an intensity parameter, it is sensitive to the input image type. A tolerance value of 10 is a good starting point for 8-bit images (with 0-255 intensity range) but it should be drastically increased when using image types with larger intensity ranges. For example to \~2000 when working on a 16-bit image (intensity values between 0 and 65535).
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{% include notice icon="note" content="Since the tolerance is an intensity parameter, it is sensitive to the input image type. A tolerance value of 10 is a good starting point for 8-bit images (with 0-255 intensity range) but it should be drastically increased when using image types with larger intensity ranges. For example to \~2000 when working on a 16-bit image (intensity values between 0 and 65535)." %}
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-**Calculate dams**: un-check this option to produce segmentations without watershed lines.
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-**Connectivity**: voxel connectivity (4-8 in 2D, and 6-26 in 3D). Selecting non-diagonal connectivity (4 or 6) usually provides more rounded objects.
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-**Merge labels**: merge together labels selected by either the **"freehand" selection too**l (on a single slice) **or the point tool** (on single or multiple slices). The zero-value label belongs to the watershed dams, therefore it will ignored in case of being selected. The first selected label value will be assigned to the rest of selected labels, which will share its color.
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<b><spanstyle="color:#f80000">Note</span></b>: to select labels on different slices, use the point selection tool and keep the SHIFT key pressed each time you click on a new label.
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{% include notice icon="note" content="To select labels on different slices, use the point selection tool and keep the SHIFT key pressed each time you click on a new label." %}
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-**Shuffle colors**: randomly re-assign colors to the labels. This is a very handy option whenever two adjacent labels present a similar color.
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@@ -177,17 +175,17 @@ The complete list of commands is as follows:
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Morphological Segmentation is part of the [MorphoLibJ](/plugins/morpholibj) library. To install it, you just need to [ add](/update-sites/following#add-update-sites) the IJPB-plugins update site:
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1\) Select {% include bc path='Help | Update...'%} from the Fiji menu to start the updater.
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1. Select {% include bc path='Help | Update...'%} from the Fiji menu to start the updater.
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2\) Click on *Manage update sites*. This brings up a dialog where you can activate additional update sites.
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2. Click on *Manage update sites*. This brings up a dialog where you can activate additional update sites.
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3\) Activate the IJPB-plugins update site and close the dialog. Now you should see an additional jar file for download.
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3. Activate the IJPB-plugins update site and close the dialog. Now you should see an additional jar file for download.
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4\) Click *Apply changes* and restart Fiji.
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4. Click *Apply changes* and restart Fiji.
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You should now find the plugin under the sub-menu {% include bc path='Plugins | MorphoLibJ | Segmentation'%}.
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**Note**: Morphological Segmentation is only one of the plugins included in the [MorphoLibJ](/plugins/morpholibj) library. By following these installation steps, you will be installing as well the rest of plugins in the suite.
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{% include notice icon="note" content="Morphological Segmentation is only one of the plugins included in the [MorphoLibJ](/plugins/morpholibj) library. By following these installation steps, you will be installing as well the rest of plugins in the suite." %}
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{% include thumbnail src='/media/plugins/photobend-demo.gif' title='Animation of the photobend time lapse (\~1500x playback speed)'%}
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There are two plugins in the collection providing two methods of crystal bending measurement: Bending\_Crystal\_Track and Laser\_Spot\_Track4. Both use the template matching technique based on OpenCV library to track the movement of specific targets in the series of time lapse images organized in the virtual stack. Direct usage of movies opened as image stacks is not supported currently (movies can be transformed in the image sequences with tools like ffmpeg. <spanstyle="color:red"> UPDATE! - movies can be used directly with the Bending\_Crystal\_Track plugin! </span> Laser\_Spot\_Track4 stil requires a series of images). Timeline of the registered process is based on exif timestamps in the images or on the constant time step if the metadata are not available.
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There are two plugins in the collection providing two methods of crystal bending measurement: Bending\_Crystal\_Track and Laser\_Spot\_Track4. Both use the template matching technique based on OpenCV library to track the movement of specific targets in the series of time lapse images organized in the virtual stack. Direct usage of movies opened as image stacks is not supported currently (movies can be transformed in the image sequences with tools like ffmpeg. <spanstyle="color:var(--fg-red)"> UPDATE! - movies can be used directly with the Bending\_Crystal\_Track plugin! </span> Laser\_Spot\_Track4 stil requires a series of images). Timeline of the registered process is based on exif timestamps in the images or on the constant time step if the metadata are not available.
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There is an ability to monitor a folder for additional images appearing in the time lapse series thus allowing live process registration. The plugins work with 8/16/32-bit greyscale or 24-bit RGB images. The matching mode can be chosen from the intensity-based or color-based for the RGB format (the later is useful for images having weak intensity contrast but possessing sufficient color gradients). Subpixel registration is available using local quadratic approximation of the matching measure.
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