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Fix usages of key include
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There are still some issues:
* Misusage of key for button presses
* Places where the key include is not used

But it's a good start!

I employed various shell scripts. Here is one for fixing places that
multiple key includes were used with explicit plus signs, rather than
passing all the keys separated by bars:

sed -i -e 's/include key keys\?='\''\([^'\'']*\)'\'' \?-\?%\} *+ *{%-\? include key keys\?='\''\([^'\'']*\)'\''/include key keys='\''\1|\2'\''/g' $(git grep -Il 'include key keys\?='\''\([^'\'']*\)'\'' \?-\?%} *+ *{%-\? include key keys\?='\''\([^'\'']*\)'\')
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ctrueden committed May 2, 2021
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4 changes: 2 additions & 2 deletions _pages/Brightness_and_Contrast.md
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Expand Up @@ -10,15 +10,15 @@ This tool may be used to adjust the brightness and contrast of an active image.

## Usage

The Brightness and Contrast tool may be accessed through {% include bc path='Image | Adjust | Brightness/Contrast'%} or {% include key content='Ctrl\|Shift\|C' %}.
The Brightness and Contrast tool may be accessed through {% include bc path='Image | Adjust | Brightness/Contrast'%} or {% include key keys='Ctrl|Shift|C' %}.

<figure><img src="/media/Brightness Contrast Window.png" title="Brightness_Contrast_Window.png" width="266" height="177" alt="Brightness_Contrast_Window.png" /><figcaption aria-hidden="true">Brightness_Contrast_Window.png</figcaption></figure>

The upper and lower limits of the display range can be adjusted by modifying the minimum and maximum settings. Image brightness and image contrast can be modified by using the brightness and contrast sliders or by using the arrows on the right of the window to adjust the range.

Selecting 'OK' will make the specified changes to the display and close the Brightness/Contrast window. All channels in an image will be simultaneously updated automatically.

ImageJ may provide intelligent thresholding based on the image's histogram through {% include bc path='Image | Adjust | Auto-Contrast'%} or {% include key content='Ctrl\|Alt\|Shift\|L' %}. Repeated usage of this process will allow more pixel values to become saturated.
ImageJ may provide intelligent thresholding based on the image's histogram through {% include bc path='Image | Adjust | Auto-Contrast'%} or {% include key keys='Ctrl|Alt|Shift|L' %}. Repeated usage of this process will allow more pixel values to become saturated.

## Example

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2 changes: 1 addition & 1 deletion _pages/Installing_3rd_party_plugins.md
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Expand Up @@ -33,7 +33,7 @@ It will ask you for the file name of the plugin, and install the given file.
- You can also copy the *.jar*, *.class* or *.java* files (or a script in any language Fiji supports) to *Fiji.app/plugins/*, followed by calling {% include bc path='Help | Refresh Menus'%}.


**Note:** On macOS, you need to {% include key content='Ctrl' %}+{% include key content='click' %} on the *Fiji* icon in the Finder and select *Show package contents* to see the *plugins/* folder.
**Note:** On macOS, you need to {% include key keys='Ctrl|click' %} on the *Fiji* icon in the Finder and select *Show package contents* to see the *plugins/* folder.

## For developers

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6 changes: 3 additions & 3 deletions _pages/Keyboard_shortcuts.md
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Expand Up @@ -13,15 +13,15 @@ For a verbose list of keyboard shortcuts, call {% include bc path='Plugins | Sho

## The Search Bar

Use {% include key content='Ctrl' %}+{% include key content='L' %} (on Mac, {% include key content='Command' %}+{% include key content='L' %}) to jump to the [search bar](/learn/getting-started#the-search-bar), to call menu entries by name.
Use {% include key key='Ctrl|L' %} (on Mac, {% include key key='Command|L' %}) to jump to the [search bar](/learn/getting-started#the-search-bar), to call menu entries by name.

## Recent Commands

To open a list of some recent commands, and a list of the most frequently called commands, hit {% include key content='Ctrl' %}+{% include key content='9' %} (on Mac, {% include key content='Command' %}+{% include key content='9' %}).
To open a list of some recent commands, and a list of the most frequently called commands, press {% include key key='Ctrl|9' %} (on Mac, {% include key key='Command|9' %}).

## Open

To open new images, type {% include key content='Ctrl' %}+{% include key content='O' %} (on Mac, {% include key content='Command' %}+{% include key content='O' %}).
To open new images, press {% include key keys='Ctrl|O' %} (on Mac, {% include key keys='Command|O' %}).

## Creating your own keyboard shortcuts

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4 changes: 2 additions & 2 deletions _pages/Project_ideas.md
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Expand Up @@ -172,7 +172,7 @@ A public Java class must be compiled from a source file reflecting the class nam

## Add a *Bookmark* function to the Script Editor

Often, it would be very convenient to remember the current cursor position to come back to, after looking around in other parts of the file. Maybe {% include key content='Ctrl' %}+{% include key content='B' %} (together with a menu entry), or {% include key content='Ctrl' %}+{% include key content='<digit>' %} are good ways to implement the user interface. (The code should be similar to the *Goto Line...* function.
Often, it would be very convenient to remember the current cursor position to come back to, after looking around in other parts of the file. Maybe {% include key keys='Ctrl|B' %} (together with a menu entry), or {% include key keys='Ctrl|<digit>' %} are good ways to implement the user interface. (The code should be similar to the *Goto Line...* function.

## Add support for Haskell (via Jaskell) and Tcl (via Jacl)

Expand Down Expand Up @@ -317,7 +317,7 @@ The code needs to be improved, though, to handle special menu items correctly, s

Some menu items are actually provided by the core of ImageJ, and it may be the best to open the appropriate place on the ImageJ website instead of the Fiji Wiki. In the alternative, the ImageJ documentation should be replicated on the Fiji Wiki under the appropriate page titles.

The user should also be informed that hitting the {% include key content='Esc' %} key gets her out of this mode.
The user should also be informed that pressing the {% include key key='Esc' %} key gets her out of this mode.

And finally, the Fiji Wiki needs some love to reflect the exact titles of the menu items, most probably by adding appropriate redirects.

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8 changes: 4 additions & 4 deletions _pages/cookbook/annotating-images.md
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Expand Up @@ -85,13 +85,13 @@ Text on converted image.

### Adding Text/Line/Box

Drawing lines/boxes is achieved by first using the line/rectangle ROI tool from the toolbar or defining the box via the *Specify Line* or *Specify ROI* plugins. The line/box can then be stamped in to the image through "*Edit/Draw*" or the shortcut {% include key content='Ctrl' %}+{% include key content='D' %}. If you're drawing the ROI on a stack, you'll be asked if you want to process all of the slices. Choosing 'yes' will draw the ROI on every slice while choosing 'no' will result in the ROI only being added to the current frame. The color is determined by the color picker toolbar button and the width in pixels is defined in "*Edit/Options/Line width*". The line width must be determined before it is drawn on the image.
Drawing lines/boxes is achieved by first using the line/rectangle ROI tool from the toolbar or defining the box via the *Specify Line* or *Specify ROI* plugins. The line/box can then be stamped in to the image through "*Edit/Draw*" or the shortcut {% include key keys='Ctrl|D' %}. If you're drawing the ROI on a stack, you'll be asked if you want to process all of the slices. Choosing 'yes' will draw the ROI on every slice while choosing 'no' will result in the ROI only being added to the current frame. The color is determined by the color picker toolbar button and the width in pixels is defined in "*Edit/Options/Line width*". The line width must be determined before it is drawn on the image.

Adding text is done with the toolbar's text button. Click the toolbar, click the image, and write the desired text. Double click on the toolbar-text button to set the font size and style. Color is determined by the color picker toolbar button. Antialiasing can be turned on/off via the menu item "*Edit/Options/Fonts*" and unchecking the "Smooth" option (although this option does not affect the Stamper plugins which have antialiasing on permanently). The text is stamped onto the image through the same methods of drawing on a box or line (*Edit/Draw* or {% include key content='Ctrl' %}+{% include key content='D' %}).
Adding text is done with the toolbar's text button. Click the toolbar, click the image, and write the desired text. Double click on the toolbar-text button to set the font size and style. Color is determined by the color picker toolbar button. Antialiasing can be turned on/off via the menu item "*Edit/Options/Fonts*" and unchecking the "Smooth" option (although this option does not affect the Stamper plugins which have antialiasing on permanently). The text is stamped onto the image through the same methods of drawing on a box or line (*Edit/Draw* or {% include key keys='Ctrl|D' %}).

It is possible to add a line, box, or text to each slice in a stack. After adding to a single slice and selecting "*Edit/Draw*", you will be asked if you want to apply the selection to every slice. Keep in mind that there is no undo option for this operation.

Adding text to a stack is a slightly different process. You can draw a text box by following the same steps, but on a stack, keyboard shortcut {% include key content='Ctrl' %}+{% include key content='B' %} will overlay the text on the current slice, while shortcut {% include key content='Ctrl' %}+{% include key content='D' %} will draw the text on every slice of the stack.
Adding text to a stack is a slightly different process. You can draw a text box by following the same steps, but on a stack, keyboard shortcut {% include key keys='Ctrl|B' %} will overlay the text on the current slice, while shortcut {% include key keys='Ctrl|D' %} will draw the text on every slice of the stack.

### Adding timestamps

Expand All @@ -103,7 +103,7 @@ Alternatively, you can also draw a rectangular ROI at the location and approxima

Remember: bigger text will typically look smoother and the timestamp will be easier to read. It may be worth changing it to a consistent value for all of your movies.

Also, bear in mind that the interval doesn't necessarily need to be "time". The Time Stamper can also be used to add "z-axis depths" to z-stacks and "angle of rotation" to rotating volume movies (° = {% include key content='Alt' %}+{% include key content='2' %}-{% include key content='4' %}-{% include key content='8' %}; µ = {% include key content='Alt' %}+{% include key content='2' %}-{% include key content='3' %}-{% include key content='0' %}).
Also, bear in mind that the interval doesn't necessarily need to be "time". The Time Stamper can also be used to add "z-axis depths" to z-stacks and "angle of rotation" to rotating volume movies (° = {% include key keys='Alt|2' %}-{% include key key='4' %}-{% include key key='8' %}; µ = {% include key keys='Alt|2' %}-{% include key key='3' %}-{% include key key='0' %}).

### Adding event markers to a movie

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8 changes: 4 additions & 4 deletions _pages/cookbook/image-intensity-processing.md
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Expand Up @@ -29,7 +29,7 @@ If you prefer the image to be displayed as "black on white" rather than "white o

If working with a stack, the ROI selected can be analyzed with the command: {% include bc path='Image | Stacks | Plot Z Axis Profile'%}. This generates a single column of numbers - one slice intensity per row.

The top 6 rows of the column are details of the ROI. This makes sure the same ROI is not analyzed twice and allows you to save any interesting ROIs. The details are comprised of area, x-coordinate, y-coordinate, AR, roundness, and solidity of the ROI. If the ROI is a polyline&gt;freehand ROI rather than a square&gt;oval, it acts as if the ROI is an oval&gt;square. The (oval) ROI can be restored by entering the details prompted by the {% include bc path='Edit | Selection | Restore Selection'%} (hotkey: {% include key content='Ctrl' %}+{% include key content='Shift' %}+{% include key content='E' %}) command.
The top 6 rows of the column are details of the ROI. This makes sure the same ROI is not analyzed twice and allows you to save any interesting ROIs. The details are comprised of area, x-coordinate, y-coordinate, AR, roundness, and solidity of the ROI. If the ROI is a polyline&gt;freehand ROI rather than a square&gt;oval, it acts as if the ROI is an oval&gt;square. The (oval) ROI can be restored by entering the details prompted by the {% include bc path='Edit | Selection | Restore Selection'%} (hotkey: {% include key keys='Ctrl|Shift|E' %}) command.

The results are displayed in a plot-window with the ROI details in the plot window title. The plot contains the buttons *List, Save, Copy.* The *Copy* button puts the data in the clipboard so it can be pasted into an Excel sheet. The settings for the copy button can be found under {% include bc path='Edit | Options | Profile Plot Options'%}. Recommended settings include: *Do not save x-values* (prevents slice number data being pasted into Excel) and *Autoclose* so that you don't have to close the analyzed plot each time.

Expand Down Expand Up @@ -67,7 +67,7 @@ Oval and rectangular ROIs can be restored individually from x, y, l, h values wi

Background subtraction is needed before analysis of dual-channel ratio images. See also the [background correction](#background-correction) section. The *Ratio\_Profiler* plugin will perform ratiometric analysis of a single ROI on a dual-channel interleaved stack. The odd-slices are channel 1 images and the even slices are channel 2 images. If your two channels are opened as separate stacks, such as Zeiss, the two channels can be interleaved (mixed together by alternating between them) with the menu command {% include bc path='Plugins | Stacks - Shuffling | Stack Interleaver'%}.

The plugin will generate a green-plot of the ratio values. Ch1÷Ch2 is the default and you can get Ch2÷Ch1 if the plugin is run with the {% include key content='Alt' %} key down. It will also generate a second plot of the intensities of the individual channels, Ch1 and Ch2, as well as a results table.
The plugin will generate a green-plot of the ratio values. Ch1÷Ch2 is the default and you can get Ch2÷Ch1 if the plugin is run with the {% include key key='Alt' %} key down. It will also generate a second plot of the intensities of the individual channels, Ch1 and Ch2, as well as a results table.

The first row of the results table contains values for the x, y, width and height of the ROI.

Expand All @@ -81,7 +81,7 @@ This table can be copied to the clipboard and pasted elsewhere with the "{% incl

2\. Open *ROI manager* ({% include bc path='Analyze | Tools | ROI manager...'%}) and click the "Show All" button.

3\. Select the cells to be analyzed and add them to the ROI manager ("Add" button or keyboard {% include key content='T' %} key).
3\. Select the cells to be analyzed and add them to the ROI manager ("Add" button or keyboard {% include key key='T' %} key).

4\. Run the plugin.

Expand Down Expand Up @@ -111,7 +111,7 @@ Linescanning involves acquiring a single line, one pixel in width, from a common

A pseudo-linescan generation of a 3-D (*x, y, t*) image. It is useful for displaying 3-D data in 2 dimensions.

A line of interest is drawn followed by the command: {% include bc path='Image | Stacks | Reslice'%} or with the keyboard button {% include key content='/' %}. It will ask you for the line width that you wish to be averaged. It will generate a pseudo-linescan "stack" with each slice representing the pseudo-linescan of a single-pixel wide line along the line of interest. Average the pseudo-linescan "stack" by selecting {% include bc path='Image | Stacks | Z-Project...'%} and use the *Average* command. A poly-line can be utilized, but this will only generate a single pixel slice.
A line of interest is drawn followed by the command: {% include bc path='Image | Stacks | Reslice'%} or with the keyboard button {% include key key='/' %}. It will ask you for the line width that you wish to be averaged. It will generate a pseudo-linescan "stack" with each slice representing the pseudo-linescan of a single-pixel wide line along the line of interest. Average the pseudo-linescan "stack" by selecting {% include bc path='Image | Stacks | Z-Project...'%} and use the *Average* command. A poly-line can be utilized, but this will only generate a single pixel slice.

Fiji's default settings assume that stacks are *z*-series rather than *t*-series. This means that many functions related to the third-dimension of an image stack are referred to with a *z-*. Just keep this in mind.

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4 changes: 2 additions & 2 deletions _pages/cookbook/t-functions.md
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Expand Up @@ -79,7 +79,7 @@ For increases in intensity (e.g. a calcium "puff") the calculation is \[Frame<su

For drops in intensity (e.g. TMRE plus irradiation induced mitochondrial depolarisations) the calculation is \[Frame<sub>n</sub> - Frame<sub>(n+1)</sub>\].

Note: The plugin generates a second result stack. For large memory consuming stacks, run the plugin with the {% include key content='Alt' %} key down. If the plugin is run with the {% include key content='Alt' %} key down, the calculation is made on the original stack. This plugin may also be useful to clean up time courses prior to motion tracking.
Note: The plugin generates a second result stack. For large memory consuming stacks, run the plugin with the {% include key key='Alt' %} key down. If the plugin is run with the {% include key key='Alt' %} key down, the calculation is made on the original stack. This plugin may also be useful to clean up time courses prior to motion tracking.

## Surface plotting

Expand All @@ -95,7 +95,7 @@ When this function is selected, a dialog will appear. Try the settings below fir

### SurfaceJ settings

You can surface plot either a single frame or a movie. Surface rendering is a slow process so it is best to pick a frame from the movie that shows the features you're trying to demonstrate. Duplicate this ({% include key content='Ctrl' %}+{% include key content='D' %}) and use it as a test image to get the best settings for surface plotting your movie.
You can surface plot either a single frame or a movie. Surface rendering is a slow process so it is best to pick a frame from the movie that shows the features you're trying to demonstrate. Duplicate this ({% include key keys='Ctrl|D' %}) and use it as a test image to get the best settings for surface plotting your movie.

Select the image to be rendered with the "*Source image(s)*" drop down box.

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2 changes: 1 addition & 1 deletion _pages/cookbook/z-functions.md
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Expand Up @@ -131,7 +131,7 @@ The window seen when 3D Viewer is opened.

To use the 3D Viewer, an 8-bit or RGB image is required. If used on another type of stack, the plugin will have a prompt for you to choose to convert to these types.

The current display mode may be changed by clicking *"Edit/Display As"*. This will let you choose from 'Volume', 'Orthoslice', 'Multi-orthoslice', 'Surface', and 'Surface Plot 2D'. When using the 'Orthoslice' mode, you can right click on the viewer and select 'Adjust Slices' to update the placement of the x, y, and z coordinates. You can also press the {% include key content='X' %}, {% include key content='Y' %}, or {% include key content='Z' %} keys in combination with arrow keys to move the slices.
The current display mode may be changed by clicking *"Edit/Display As"*. This will let you choose from 'Volume', 'Orthoslice', 'Multi-orthoslice', 'Surface', and 'Surface Plot 2D'. When using the 'Orthoslice' mode, you can right click on the viewer and select 'Adjust Slices' to update the placement of the x, y, and z coordinates. You can also press the {% include key key='X' %}, {% include key key='Y' %}, or {% include key key='Z' %} keys in combination with arrow keys to move the slices.

<figure><img src="/media/3d viewer volume.png" title="3d_viewer_volume.png" width="264" height="286" alt="3d_viewer_volume.png" /><figcaption aria-hidden="true">3d_viewer_volume.png</figcaption></figure>

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2 changes: 1 addition & 1 deletion _pages/develop/architecture.md
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Expand Up @@ -292,7 +292,7 @@ There are two easy ways of going about this:

These files need not have any content; their mere existence will trigger the dev profile associated with the named organization, causing all artifacts of that organization to become coupled as `SNAPSHOT`s.

In the case of Eclipse, you may need to "Update Maven project" in order to see the snapshot couplings go into effect; the shortcut {% include key content='Alt' %}+{% include key content='F5' %} while selecting the affected project(s) accomplishes this quickly.
In the case of Eclipse, you may need to "Update Maven project" in order to see the snapshot couplings go into effect; the shortcut {% include key keys='Alt|F5' %} while selecting the affected project(s) accomplishes this quickly.

{% include warning-box content='**Current versions of the Eclipse Maven integration (tested with Eclipse Mars) fail to correctly resolve the `LATEST` version tag to `SNAPSHOT`s. Use the command-line client instead.**' %}

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