Virtual Observatories
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SalsaJ 2 offers a new possibility: the use of amazing astronomical images, in colour. These images have been taken by the astronomers of the European Southern Observatory ESO, and can be used freely.

Here is a list of the available images with some explanations.

 

  • Alma telescope at Chajnantor: Artist rendering of the Atacama Large Millimeter/submillimeter Array (ALMA), in an extended configuration.
  • Centaurus A black Hole: This galaxy is a most interesting object for the present attempts to understand active galaxies. It is being investigated by means of observations in all spectral regions, from radio via infrared and optical wavelengths to X- and gamma-rays. On images obtained at optical wavelengths, thick dust layers almost completely obscure the galaxy's centre. This structure was first reported by Sir John Herschel in 1847. Until 1949, NGC 5128 was thought to be a strange object in the Milky Way, but it was then identified as a powerful radio galaxy and designated Centaurus A. The core of Centaurus A is the smallest known extragalactic radio source, only 10 light-days across. A jet of high-energy particles from this centre is observed in radio and X-ray images. The core probably contains a supermassive black hole with a mass of about 100 million solar masses.
  • Chandra deep field with many galaxies: observations were made over a period of 40 hours and constitute the deepest image ever taken from the ground in the U-band. The image shows galaxies that are 1 billion times fainter than can be seen by the unaided eye.
  • Christmas Tree NGC2264: This colour image of the region known as NGC 2264 — an area of sky that includes the sparkling blue baubles of the Christmas Tree star cluster and the Cone Nebula — was created from data taken through four different filters (B, V, R and H-alpha) with the Wide Field Imager at ESO's La Silla Observatory, 2400 m high in the Atacama Desert of Chile in the foothills of the Andes. The image shows a region of space about 30 light-years across.
  • Crab Nebula M1:This photo shows a three colour composite of the well-known Crab Nebula (also known as Messier 1). It is the remnant of a supernova explosion at a distance of about 6,000 light-years, observed almost 1,000 years ago, in the year 1054. It contains a neutron star near its center that spins 30 times per second around its axis. In this picture, the green light is predominantly produced by hydrogen emission from material ejected by the star that exploded. The blue light is predominantly emitted by very high-energy ("relativistic") electrons that spiral in a large-scale magnetic field (so-called syncrotron emission). It is believed that these electrons are continuously accelerated and ejected by the rapidly spinning neutron star at the centre of the nebula and which is the remnant core of the exploded star. This pulsar has been identified with the lower/right of the two close stars near the geometric center of the nebula, immediately left of the small arc-like feature.
  • Dumbbell Nebula: The Dumbbell Nebula - also known as Messier 27 or NGC 6853 - is a typical planetary nebula and is located in the constellation Vulpecula (The Fox). The distance is rather uncertain, but is believed to be around 1,200 light-years. It was first described by the French astronomer and comet hunter Charles Messier who found it in 1764 and included it as no. 27 in his famous list of extended sky objects [2] .Despite its class, the Dumbbell Nebula has nothing to do with planets. It consists of very rarified gas that has been ejected from the hot central star (well visible on this photo), now in one of the last evolutionary stages. The gas atoms in the nebula are excited (heated) by the intense ultraviolet radiation from this star and emit strongly at specific wavelengths.
  • Eagle Nebula: Messier 16 (M16), also known as the Eagle Nebula, is located in the southern constellation of Serpens (the Snake). The wide-field view of M16 shows that there is much happening in the region. The first impression one gets is of an enormous number of stars. Those which are blue in the infrared image are either members of the young NGC 6611 cluster — whose massive stars are concentrated in the upper right (north west) part of the field — or foreground stars which happen to lie along the line of sight towards M16.Most of the stars are fainter and more yellow. They are ordinary stars behind M16, along the line of sight through the galactic bulge, and are seen through the molecular clouds out of which NGC 6611 formed. Some very red stars are also seen : these are either very young and embedded in gas and dust clouds, or just brighter stars in the background shining through them.
  • Eta Carinae: This new image of the luminous blue variable Eta Carinae was taken with the NACO near-infrared adaptive optics instrument on ESO's Very Large Telescope, yielding an incredible amount of detail. The images clearly shows a bipolar structure as well as the jets coming out from the central star.
  • Flame Nebula: This image, the first to be released publicly from VISTA, the world’s largest survey telescope, shows the spectacular star-forming region known as the Flame Nebula, or NGC 2024, in the constellation of Orion (the Hunter) and its surroundings. In views of this evocative object in visible light the core of the nebula is completely hidden behind obscuring dust, but in this VISTA view, taken in infrared light, the cluster of very young stars at the object’s heart is revealed. The wide-field VISTA view also includes the glow of the reflection nebula NGC 2023, just below centre, and the ghostly outline of the Horsehead Nebula (Barnard 33) towards the lower right. The bright bluish star towards the right is one of the three bright stars forming the Belt of Orion.
  • Galactic Center: The central parts of our Galaxy, the Milky Way, as observed in the near-infrared with the NACO instrument on ESO's Very Large Telescope. By following the motions of the most central stars over more than 16 years, astronomers were able to determine the mass of the supermassive black hole that lurks there.
  • Helix Nebula: This colour-composite image of the Helix Nebula (NGC 7293) was created from images obtained using the the Wide Field Imager (WFI), an astronomical camera attached to the 2.2-metre Max-Planck Society/ESO telescope at the La Silla observatory in Chile. The blue-green glow in the centre of the Helix comes from oxygen atoms shining under effects of the intense ultraviolet radiation of the 120 000 degree Celsius central star and the hot gas. Further out from the star and beyond the ring of knots, the red colour from hydrogen and nitrogen is more prominent. A careful look at the central part of this object reveals not only the knots, but also many remote galaxies seen right through the thinly spread glowing gas.
  • Horsehead Nebula: A reproduction of a composite colour image of the Horsehead Nebula and its immediate surroundings.
  • Jewel Box cluster NGC4755: The FORS1 instrument on the ESO Very Large Telescope (VLT) at ESO’s Paranal Observatory was used to take this exquisitely sharp close up view of the colourful Jewel Box cluster, NGC 4755.
  • Milky Way: This magnificent 360-degree panoramic image, covering the entire southern and northern celestial sphere, reveals the cosmic landscape that surrounds our tiny blue planet. This gorgeous starscape serves as the first of three extremely high-resolution images featured in the GigaGalaxy Zoom project, launched by ESO within the framework of the International Year of Astronomy 2009 (IYA2009). The plane of our Milky Way Galaxy, which we see edge-on from our perspective on Earth, cuts a luminous swath across the image. The projection used in GigaGalaxy Zoom place the viewer in front of our Galaxy with the Galactic Plane running horizontally through the image — almost as if we were looking at the Milky Way from the outside. From this vantage point, the general components of our spiral galaxy come clearly into view, including its disc, marbled with both dark and glowing nebulae, which harbours bright, young stars, as well as the Galaxy’s central bulge and its satellite galaxies. As filming extended over several months, objects from the Solar System came and went through the star fields, with bright planets such as Venus and Jupiter.
  • New planetary system Gliese 581
  • Omega Centauri
  • Orion Nebula
  • Pair of Galaxies NGC1532
  • Pluto artiste view
  • Sombrero Galaxy
  • Spiral Galaxy Messier 83
  • Spiral Galaxy NGC1232
  • Spiral Galaxy NGC253
  • Spiral Galaxy NGC300
  • Spiral Galaxy NGC4945
  • Starburst Region NGC3603
  • Star R Coronae Australis
  • Stellar cluster NGC2467
  • Stellar Nursery
  • The Moon
  • Trifid Nebula
  • VLT Paranal platform
  • VLT Paranal with laser

 

Keyboard Shortcuts
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Command Shortcut Description
New N Creates a new image or stack
Open O Opens a TIFF, GIF, JPEG, BMP, DICOM or FITS
Open Samples Shift-B Opens "Blobs" example image
Close W Closes the active window
Save S Saves active image in Tiff format
Revert R Revert to saved version of image
Print P Print active image
     
Undo Z Reverses the effect of the last operation
Cut X Copy image to clipboard and clear selection
Copy C Copy image to clipboard
Paste V Paste clipboard selection into active image
Clear backspace Erases selection to background color
Select All A Select entire image
Select None Shift-A Delete selection
Restore Selection Shift-E Restores ROI
Fill F Fills selection in foreground color
Draw D Draw selection
Invert Shift-I Invert image or selection
     
Adjust Contrast Shift-C Adjust brightness and contrast
Adjust Threshold Shift-T Adjust threshold levels
Show Info I Displays information about active image
Next Slice > Advance to next stack slice
Previous Slice < Backup up to previous stack slice
Start Animation = Starts/stops stack animation
Duplicate Shift-D Duplicates active image or selection
Scale E Scale image or selection
     
Smooth Shift-S 3x3 unweighted smoothing
Find Edges Shift-F Performs Sobel edge detection
Repeat Command Shift-R Repeats previous command
     
Measure M Displays statistics about active image or selection
Histogram H Displays a histogram of the active window or selection
Plot Profile K Displays density profile plot of current selection
ImageJ enter Brings ImageJ window to front
Put Behind tab Switches to next image window

Alt Key Modifications
   Image/Adjust/Threshold: Adjusting Min also adjusts Max
   Image/Stacks/Add Slice: Insert before current slice
   Image/Stacks/Next Slice: Skip nine slices
   Image/Stacks/Previous Slice: Skip nine slices
   Image/Duplicate: Don't show dialog
   Image/Colors: Alt-click to "pick up" background color
   Process/Equalize: Do classic histogram equalization
   Process/Subtract Background: Show background image
   Analyse/Plot Profile: For rectangular selections, generate row average plots
   Analyse/Tools/Analyse Line Graph: Show intermediate image
   Plugins/Utilities/ImageJ Properties: List all Java properties
   Plugins/Utilities/Monitor Memory: Simulate 640x480 frame grabber
   Any User Plugin: Load using new class loader

Space Bar Modifications
   Any Tool: Temporarily switch to the "hand" (scrolling) tool
   Moving through a stack: Automatically adjust min/max display values

Arrow Keys
Use the arrow keys to move selection outlines one pixel at a time. Resize rectangular and oval selections by holding down the the alt (option) and while using the arrow keys.

Window Menu
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This menu contains two commands plus a list of open SalsaJ windows. The currently active image will have a checkmark next to its name. To activate a window, pull down this menu and select the window by name.

SalsaJ [enter]
Press the enter key to bring the SalsaJ window to the front.

Put Behind [tab]
Displays the next open image. Repeatedly press the tab key to cycle through all open images.

Tools
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http://www.euhou.net/docupload/files/software/manuel/tools_fichiers/toolbare.jpg


File/New...
File/Open...
File/Save
File/Save As/Fits...
File/Print...
Edit/Clear
Edit/Undo
Image/Adjust/Brightness/Contrast...
Analyse/Photometry
Analyse/Photometry Settings
Analyse/Clear Photometry Results
Help/Online Docs...

 

Area Selection Tools
Use these tools to create area selections that will be operated on separately from the rest of the image. The contents of an area selection can be copied to the internal clipboard, cleared (to white), filled with the current drawing colour, outlined (using Edit/Draw), filtered, or measured. Use the backspace key as a shortcut for Edit/Clear. Use Image/colours to set the drawing colour. Double click on any line tool to change the line width used by Edit/Draw. Use the arrow keys to "nudge" a selection one pixel at a time in any direction.

Rectangle
When creating the selection, drag with the shift key down to constrain it to a square. Use the small "handle" in the lower right corner to resize. Use the arrow keys with the alt key held down to change the width or height one pixel at a time. As a selection is created or resized, its location, width and height are displayed in the status bar.

 Oval
Creates an elliptical selection. Holding the alt key down forces the selection to be circular. Use the arrow keys with the alt key pressed to change the width or height. As the selection is created or resized, its width and height are displayed in the status bar.

 Polygon
Creates irregularly shaped selections defined by a series of line segments. To create the selection, click repeatedly with the mouse to create line segments. When finished, click in the small box at the starting point (or double-click), and SalsaJ automatically draws the last segment.

 Freehand
The freehand tool lets you create irregularly shaped selections by dragging with the mouse.

Isovaluated Selection Tool
Creates a selection by tracing objects of uniform colour or thresholded objects. To trace an object, either click inside near the right edge, or outside to the left of the object. To visualize what happens, imagine a turtle that starts moving to the right from where you click looking for an edge. Once it finds the edge, it follows it until it returns to the starting point. Note that the wand tool may not reliably trace some objects, especially one pixel wide lines, unless they are thresholded (highlighted in red) using the Image/Adjust/Threshold tool. 

 

Line Selection Tools
Use these tools to create line selections. Use analyse/Measure to calculate the length of a line selection. Use Edit/Draw to permanently draw the line on the image. Change the drawing colour by clicking in the Image/colours window. Double click on any line tool to specify the line width. Use the arrow keys to "nudge" a line selection one pixel at a time.

 Straight Line
Use this tool to create a straight line selection. Holding the alt key down forces the line to be horizontal or vertical. To spatially calibrate an image, create a line selection corresponding to a known distance (e.g. 10mm), then enter that distance in the analyse/Set Scale dialog box. PlugIns/Draw Arrow will draw an arrow based on a straight line selection.

Segmented Line
Create a segmented line selection by repeatedly clicking with the mouse. Each click will define a new line segment. Double-click when finished.

 Freehand Line
Select this tool and drag with the mouse to create a freehand line selection.

Angle
Create an angle selection by clicking Three times with the mouse. The first twocreate the first straight line of the angle and the last creates the second. The value of the angle is displayed during the construction in the status bar.

Point Selection Tool

Use this tool to create a point selection and to display coordinates and value in a new window. Click once to create a single point selection. Click to add more points.  Alt-click on a point to delete it.  Double-click on the point tool icon to display the following configuration dialog box.


                   

 Text Tool
Use this tool to add text to images. It creates a rectangular selection containing one or more lines of text. Use the keyboard to add characters to the text and the backspace key to delete characters. Use Edit/Draw to permanently draw the text on the image. Use Edit/Options/Fonts, or double-click on the text tool, to specify the typeface, size and style.

Magnifying Glass
Click on the image with this tool to zoom in. Alt-click (or right-click) to zoom out. The current magnification is shown in the image's title bar. Double-click on the magnifying glass icon to revert to 100% (1:1) magnification. There are 20 possible magnification levels: 3.1, 4.2, 6.3, 8.3, 12.5, 16.7, 25, 33.3, 50, 75, 100, 200, 300, 400, 600, 800, 1200, 1600, 2400 and 3200 percent. When zooming in, press the shift key to prevent the window from being enlarged.

 Scrolling Tool
Allows you to scroll through an image that is larger than its window. When using other tools (except the text tool), you can temporarily switch to this tool by holding down the space bar.

Colour Picker
Sets the foreground drawing colour by "picking up" colours from images. The colour of this tool's icon changes to match the drawing colour. colours can "picked up" from the Image/colours window using any tool. Alt-click in the Image/colours window to change the background colour. Double-click on this tool to display the Image/colours window. he icon for this tool is drawn in the current foreground colour and the frame around it is drawn in the current background colour.

Plugins Menu
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Introduction

Plugins and macros are loadable code modules that extend the capabilities of SalsaJ. Plugins are written in the Java programming language and compiled to .class files. Macros, written in SalsaJ's Java-like macro language, are stored in .txt files. Plugins run faster and are more flexible but macros are easier to write and debug. Plugins and macros in the plugins folder, with an underscore in their name, are listed at the bottom of this menu. Plugins and macros in subfolders of the plugins folder are listed in submenus. Use Shortcuts/Create Shortcut to assign a keyboard shortcut to a plugin or a macro.

Use the Record command to record a series of commands and to convert them to a macro. Use the New command to create a new macro or plugin and Edit to make changes to an existing one. More than 100 plugins are available on the ImageJ Web site as well as more than 80 macros. A tutorial for plugin writers is available at http://mtd.fh-hagenberg.at/depot/imaging/imagej/. Information about macros is available on the ImageJ Web site.

Internal Plugins
Most commands in SalsaJ are implemented as plugins but these internal plugins are located in the salsaj.jar file, not in the plugins folder. salsaj.jar also contains the properties file (IJ_Props.txt) that SalsaJ uses to install internal plugins in menus. A JAR file (Java ARchive) is formatted the same as a ZIP file, so you can use a ZIP utility to look at the contents of salsaj.jar.

You can convert an internal plugin to a user plugin by copying the source to the plugins folder, adding an underscore to the file name and class name, and changing the package statement to an import statement. For example, to change the RoiManager (analyse/Tools/ROI Manager) to a user plugin:

  1. Copy ij/plugin/frame/RoiManager.java to the plugins folder.
  2. Change the file name to Roi_Manager.java.
  3. Open Roi_Manager.java using Plugins/Edit and change all instances (4) of "RoiManager" to "Roi_Manager".
  4. Change the first line from "package ij.plugin.frame;" to "import ij.plugin.frame.*;".
  5. Run the new plugin using the editor's File/Compile and Run command.
There will be a new Roi Manager command in the Plugins menu the next time you restart SalsaJJ.

Changing Location of Plugins Directory
The "plugins.dir" property specifies the location of the parent of the plugins directory. This property can be set from either the command line or from within a Java program that starts SalsaJ. For example, if you run SalsaJ with the command

java -Dplugins.dir=/Users/wayne -cp ij.jar ij.ImageJ
it will look for the plugins folder in the /Users/wayne/ directory. This property can also be set in a program that launches SalsaJ:
System.getProperties().setProperty("plugins.dir", "/users/wayne");
new ImageJ(null);

Macros>
This submenu contains commands for installing, running and recording macros, as well as any macro commands added by Plugins/Macros/Install. Macros contained in a file named "StartupMacros.txt", in the macros folder, are automatically added to this submenu when SalsaJ starts up.

Install...
Adds one or more macros contained in a file to the bottom of this submenu. To install a set of macros, and at the same time view their source code, open the macro file with File/Open and use the editor's Macros/Install Macros command. Macros in the file ImageJ/macros/StartupMacros.txt are automatically installed when SalsaJ starts up.

Run...
Loads and runs a macro without opening it in the SalsaJ editor. To run a macro, and at the same time view its source code, open it with File/Open and use the editor's File/Run Macro command.

Record...
Opens the SalsaJ command recorder. To create a macro, open the recorder, use one or more SalsaJ commands, then click "Create". When the recorder is open, each menu command you use generates a macro run() function call. The run() function has one or two string arguments. The first is the command name. The optional second argument contains dialog box parameters.

Create a rectangular, oval or line selection and the recorder will generate a makeRectangle(), makeOval() or makeLine() function call. Click on "Auto" or "Set" in the Image/Adjust/Threshold window to generate a setThresold() call, and on "Reset" to generate a resetThresold() call. Select an image from the Window menu to generate a selectWindow() call. Click in the Image/colour/colour Picker window to generate setForegroundcolour() and setBackgroundcolour() calls.

Shortcuts>
This submenu contains commands for creating keyboard shortcuts and for installing and removing plugins.

Create Shortcut...
Assigns a keyboard shortcut to an SalsaJ menu command and lists the shortcut in the Shortcuts submenu.

Select the command from the popup menu and enter the shortcut in the text field. A shortcut can be a lower or uppercase letter or "F1" through "F12". Use Plugins/Utilities/List Shortcuts to get a list of shortcuts that are already being used.

Install Plugin...
Installs a plugin in a user-specified submenu. Plugins with a showAbout() method are also automatically added to the Help/About Plugins submenu.

Use the first popup menu to select the plugin and the second to select the submenu it is to installed in. The command must be different from any existing SalsaJ command. Shortcut (optional) must be a single letter or "F1" through "F12". Argument (optional) is the string that will passed to the plugin's run method.

Remove...
Removes commands added to the Shortcuts submenu by Create Shortcuts. Also removes commands added by Install Plugin and removes plugins installed in the Plugins menu. The menus are not updated until SalsaJ is restarted.

Utilites>

Control Panel...
This command opens a window containing SalsaJ commands in a hierarchical tree structure. Click on a leaf node to launch the corresponding SalsaJ command (or plugin). Double-click on a tree branch node (folder) to expand or collapse it. Click and drag on a tree branch node (folder) to display its descendants in a separate (child) window. In a child window, click on "Show Parent"to re-open the parent window. The Control Panel was contributed to the imageJ project by Cezar M. Tigaret.

Control Panel

Monitor Memory...
Displays a continuously updated graph of SalsaJ's memory utilisation, which can be useful for detecting memory leaks. Ideally you should be able to open a several images, process them, close them, and the amount of memory used will be the same as when you started. Clicking on SalsaJ's status bar, which forces the Java garbage collector run, may help reclaim unused memory. Start the memory monitor with the alt key down to have it use a 640x480 window that simulates how a frame grabber plugin would work.

Capture Screen
Copies the the screen to an RGB image and displays that image a new window. Pressing control-shift-g will capture the screen while a modal dialog box is active if the dialog is based on SalsaJ's GenericDialog class.

New...
Opens a new text window containing a prototype (as Java source code) for one of the three types of plugins supported by SalsaJ.

PlugIn: Opens, captures or generates images. Implements the PlugIn interface. The prototype displays "Hello world!" in the SalsaJ window. Another example is the Step Maker plugin at http://rsb.info.nih.gov/ij/plugins/steps.html.

PlugInFilter: Processes the active image. Implements the PlugInFilter interface. The prototype inverts the active image twice. Another example is the Image Inverter plugin at http://rsb.info.nih.gov/ij/plugins/inverter.html.

PlugInFrame: Displays a nonimage window containing controls such as buttons and sliders. Extends the PlugInFrame class. The prototype opens a window containing a text area. Another example is the IP Demo plugin at http://rsb.info.nih.gov/ij/plugins/ip-demo.html.

The text window created by this command has two menus: File and Edit. Use Compile and Run in the File menu to compile and run the plugin. The Edit menu does not contain Cut/Copy/Paste but the keyboard shortcuts for these function can be used. Note that the name you choose for the plugin must include at least one underscore.

Edit...
Opens a text window that allows you to edit, compile and run plugins. Like the Compile and Run command, it requires that SalsaJ be running on a Java Virtual Machine that includes the javac compiler.

Compile and Run...
Compiles and runs a plugin. Requires that SalsaJ be running on a Java Virtual Machine that includes the javac compiler. Javac is included with the Windows and Linux versions of SalsaJ that come bundled with a Java runtime. It is also included with Mac OS X Java. Users of Sun's Java 2 SDK (Software Development Kit) for Windows, Linux and Solaris must add tools.jar to the command line that runs SalsaJ. 

Here is an example Windows command line for running SalsaJ using the Java 2 SDK (aka JDK):

java -mx100m -cp salsaj.jar;C:\jdk1.4\lib\tools.jar ij.ImageJ
It assumes the Java 2 SDK is installed in C:\jdk1.4. On a Unix system, the command would look something like this:
java -mx100m -cp salsaj.jar:\usr\local\jdk1.4\lib\tools.jar ij.ImageJ
The -mx100 options specifies that SalsaJ can use up to 100MB of RAM. To avoid virtual memory thrashing, this value should not be set to more than 2/3 of available RAM (e.g. -mx170m on a 256MB machine).

On Windows, you can create a double-clickable shortcut that uses Java 2 to run SalsaJ:

  1. Right-click on the desktop and select New->Shortcut from the menu
  2. Enter     
         javaw -mx100m -cp salsaj.jar;C:\jdk1.4\lib\tools.jar ij.ImageJ
    as the "Command line"; click "Next"
  3. Enter a name for the shortcut (e.g. "SalsaJ"); click "Finish"
  4. Right-click of the newly created shortcut and select Properties from the menu
  5. Click on the Shortcut tab
  6. Enter the path to the SalsaJ folder (normally C:\SalsaJ) in "Start in"; click "OK"
"javaw" is a variation of the java command that runs Java applications without a DOS window.