Image Menu
Type>  
Use this submenu to determine the type of the active image or to convert it to another type. For more informations about the types of bitmap image, consult this link.

8-bit
Converts to 8-bit grayscale. The active image must be 16-bit grayscale, 32-bit grayscale, 8-bit colour or RGB colour.

SalsaJ converts 16-bit and 32-bit images to 8-bits by linearly scaling from min-max to 0-255, where min and max are the two values displayed in the Image/Adjust/Brightness/Contrast tool. Image/Show Info displays these two values as the "Display range". Note that this scaling is not done if "Scale When Converting" is not checked in Edit/Options/Miscellaneous. With stacks, all the slices are scaled to 8-bits using the min and max of the currently displayed slice.

RGB images are converted to grayscale using the formula gray=0.299red+0.587green+0.114blue or the formula gray=(red+green+blue)/3 if "Unweighted RGB to Grayscale Conversion" is checked in Edit/Options/Conversions.

16-bit
Converts to unsigned 16-bit grayscale. The active image must be 8-bit grayscale or 32-bit grayscale.

32-bit
Converts to signed 32-bit floating-point grayscale. The active image must be 8-bit grayscale or 16-bit grayscale.

8-bit Colour
Converts to 8-bit indexed colour using Heckbert's median-cut colour quantization algorithm. A dialog box allows the number of colours (2-256) to be specified. The active image must be RGB colour.

RGB Colour
Converts to 32-bit RGB colour. The active image must be grayscale, 8-bit Colour, or an RGB (red, green, blue) or HSB (hue, saturation and brightness) stack.

RGB Stack
Converts to a 3-slice (red, green, blue) stack. The active image must be RGB colour.

HSB Stack
Converts to a 3-slice (hue, saturation and brightness) stack. The active image must be RGB colour.

An attempt to perform an unsupported conversion causes a dialog box to be displayed that lists the possible conversions. The * indicates that both single images and stacks can be converted.


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Adjust>
This submenu contains commands that adjust brightness/contrast, threshold levels and image size.

Brightness/Contrast...
Use this tool to interactively alter the brightness and contrast of the active image. With 8-bit images, brightness and contrast are changed by updating the image's look-up table (LUT), so pixel values are unchanged. With 16-bit and 32-bit images, the display is updated by changing the mapping from pixel values to 8-bit display values, so pixel pixel values are also unchanged. Brightness and contrast of RGB images are changed by modifying the pixel values. (For more information about the types of bitmap image, consult this
link)

 Press shift-c to open the B&C window the quick and easy way. If it is already open, it is activated.

b&c

The line graph at the top of the window, which us superimposed on the image's histogram, shows how pixel values are mapped to 8-bit (0-255) display values. The two numbers under the plot are the minimum and maximum displayed pixel values. These two values define the display range, or "window". SalsaJ displays images by linearly mapping pixel values in the display range to display values in the range 0-255. Pixels with a value less than the minimum are displayed as black and those with a value greater than the maximum are displayed as white.

There are four sliders. Minimum and Maximum control the lower and upper limits of the display range. Brightness increases or decreases image brightness by moving the display range. Contrast increases or decreases contrast by varying the width of the display range. The narrower the display range, the higher the contrast.

Click on Auto, and SalsaJ will automatically optimizes brightness and contrast based on an analysis of the image's histogram. Create a selection, and the entire image will be optimized based on an analysis of the selection. The optimization is done by allowing a small percentage of pixels in the image to become saturated (displayed as black or white). Each additional click on Auto increases the number of saturated pixels and thus the amount of optimization.

Click on Reset to restore the original brightness and contrast settings. The display range is set to the full pixel value range of the image. 

Click on Set to enter the minimum and maximum display range values in a dialog box. A setMinAndMax() macro call is generated if the command recorder is running.

setminmax

Click on Apply to apply the current display range mapping function to the pixel data. If there is a selection, only pixels within the selection are modified. This option currently only works with 8-bit images and stacks and with RGB stacks. This is the only B&C option that alters the pixel data of non-RGB images.

Threshold...
Use this tool to interactively set lower and upper threshold values, segmenting the image into features of interest and background. Pixels with brightness values greater than or equal to the lower threshold and less than or equal to the upper threshold are displayed in red (example 1 with the file "Elephant.fits") . If Over/Under is selected in the popup menu,
pixels with brightness values greater than or equal to the upper threshold are displayed in green and less than or equal to the lower threshold in blue (example 3).If Useanalyse/Measure (with "Limit to Threshold" in analyse/Set Measurements checked) to measure the aggregate of the selected features. Use analyse/analyse Particles to measure features individually. Use the wand tool to outline a single featurepixels with brightness values greater than or equal to the upper threshold and less than or equal to the lower threshold are displayed in green.

example 1 :

threshold thresholdElephant


example 2 :

                                    
 example 3 :


Use the upper slider to adjust the minimum threshold value and the lower one to adjust the maximum. Hold the alt key down while adjusting the minimum to move a fixed-width thresholding window across the range of gray values.

The Auto button automatically sets the threshold levels based on an analysis of the histogram of the current image or selection. Apply sets thresholded pixels to black and all other pixels to white. Reset disables thresholding and update the histogram. B&W switches to a mode where features are displayed in black and background in white (example 2). Click on Set (not shown) to enter new threshold levels into a dialog box.

Size...
Scales the active image or selection to a specified width and height in pixels.


Check Constrain Aspect Ratio to create an image with the specified width and have SalsaJ adjust the height to maintain the original aspect ratio. Check Interpolate to use bilinear interpolation. Set New width to 0 to create an image with the specified height and have SalsaJ adjust the width to maintain the original aspect ratio.

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Show Info...
Opens a text window containing information about the active image. For DICOM and FITS images, also displays file header information. Use the popup menu (right-click in the Info window) to save the information to a text file or copy it to the system clipboard.


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colour>

Convert Stack to RGB
Converts a 2 or 3-slice stack to an RGB image. The stack must be 8-bit or 16-bit grayscale.

 


RGB Split
Separate an RGB image into 3 images in  8-bit or 16-bit grayscale.




                 

RGB Merge....

Merge 3 images to an RGB image. The images must be 8bit or 16-bit grayscale. In fact, it's an opposite tool of RGB Split.
Opens a small window with three popup menus for specifying the 3 images.

   
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Stacks>
This submenu contains commands that work with stacks.


                     


Add Slice
Inserts a blank slice after the currently displayed slice. Hold down the alt key to add the slice before the current slice.


Delete Slice
Deletes the currently displayed slice.

Next Slice
Displays the slice that follows the currently displayed slice. As a shortcut, press the ">" key.

Previous Slice
Displays the slice that precedes the currently displayed slice. As a shortcut, press the "<" key.

Set Slice...
Displays a specified slice. The user must enter a slice number greater than or equal to one and less than or equal to the number of slices in the stack.


Convert Images to Stack
Creates a new stack consisting of all images currently displayed in separate windows. The images must all be the same type and size.


Convert Stack to Images
Converts the slices in the current stack to separate image windows.

Make Montage
Produces a single image which contains the images from a stack displayed in a grid format. This can be useful for visual comparisons of a series of images stored in a stack. A dialog box allows you to specify the magnification level at which the images are copied, and to select the layout of the resulting grid.

 






Start Animation
Animates the active stack by repeatedly displaying its slices (frames) in sequence. Use Stop Animation, or click with the mouse, to stop. Use the Animation Options dialog box to specify the animation speed. More than one stack can be animated at a time. As a shortcut, press the "=" key to start animation.

Show Animation

Stop Animation
Terminates animation of the active stack.

Animation Options...
Use this dialog to set the animation speed in frames per second or to enable "oscillating" animation.

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Crop
Crops the image or stack based on the current rectangular selection.

      
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Duplicate
Creates a new window containing a copy of the active image or rectangular selection. Hold the alt key down to skip the dialog box.

   
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Scale...
Resizes the image or selection horizontally and/or vertically by scale factors entered into a dialog box. Check Interpolate to scale using bilinear interpolation. Use integer scale factors (2, 3, 5, etc.) for the best looking results, particularly with graphics and text. With scale factors less then 1.0, smoothing the source image prior to scaling may produce better looking results.


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Lookup Tables>
This submenu contains a selection of colour lookup tables that can be applied to grayscale images to produce false-colour images.  More than 100 additional lookup tables are available at
rsb.info.nih.gov/ij/download/luts/.
For example :

init "LUT Green" 
"LUT  Spectrum" "LUT Blue"
"LUT Red"

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Show LUT
Displays a plot of the active image's lookup table. The lookup table, or colour table, describes the colour that is displayed for each of the 256         possible pixel values. For 16 and 32 bit images, the range of displayed pixel values is mapped to 0-255. Note that RGB colour images do not         use a lookup table.

          

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        Invert LUT
       
    Inverts the current lookup table. For 8-bit images, the value (v) of each entry in the table is replaced by 255-v. With inverted LUTs, pixels with a value of zero are white and pixels with a value 255 are black. Unlike the Edit/Invert command, pixels values are not altered, only the way the image is displayed on the screen. 

   

                  
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