“JEOL Raw File Opener” Plugin for NIH ImageJ Running
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1. Select Cancel Figure 2 Directory selection window JEOL Raw File Opener Plugin Manual Solaris version ImgJOO1 S It needs to be stressed that the user does not select the individual images but selects the sample directory in which the image files are stored When the user is working across a network it is necessary to first select the network drive from the Look In pull down at the top of the directory selection window If the program is doing bulk conversions the user will then be asked to select an output directory Map Selection Window Once the sample directory has been selected the Map Selection window will open Figure 3 This window allows the user to select single or multiple stage positions to be converted depending on the program mode If the images are to be opened in ImageJ the user can select one Stage position by clicking on it in the selection window or by entering the stage position number in the Starting Map box In this mode the Last Map box is disabled In the Bulk Conversion mode the user can either enter the starting and ending stage positions in the Starting Map and Last Map boxes respectively or they can select multiple sets from the selection window LET SEE Please Select Start and End Maps Sample Groupe NorthemShield img mi m rity mg mg X Ray Figure 3 Map Selection window Shift click allows for multiple co2. JEOL Raw File Opener Plugin for NIH ImageJ Running on Sun Solaris from McSwiggen amp Associates Background Many JEOL 8900 and 8200 users have asked for an easier way to convert JEOL image files to TIFF formats They have asked for a method that does not involve screen capturing that can display micron markers on the images and that can convert many images in a batch manner It was felt that the most direct way to do this was to use the existing program ImageJ and to write a custom plugin that would be able to read the JEOL file structures A plugin called JEOL Raw File Opener has been written for this purpose It allows JEOL users to open and convert JEOL images X ray maps into TIFF or JPEG formats The plugin can either read the file into ImageJ where it can be further manipulated before being saved into the desired format or the plugin can be used to convert an entire JEOL Sample of images The plugin was designed with three main objectives 1 Allow the user to open a JEOL image file without requiring the user to input the various image parameters The plugin will read the condition files and determine all of the required parameters for reading the individual image files 2 Use the information from the image conditions files to properly scale the image and if selected to display a scale bar on the image 3 Allow the user to select a directory containing JEOL image files and save all of the images as TIFF or JP
3. It is hoped that the Macintosh version will also become an option in the future JEOL Raw File Opener was written by Glenn Poirier for McSwiggen amp Associates and is not a product of JEOL USA Inc or JEOL Ltd Sun Solaris Installation 1 Open a terminal window 2 Log in as superuser gt SU gt password 3 Change the directory pointer to the CDROM gt cd cdrom imagej_plugin If you can t find it then try gt cd cdrom gt Is This should list the name of the cdrom in the machine Now change the directory to that cd using gt cd lt cdname gt 4 Run the enclosed shell script gt setup sh 5 When the main menu comes up select 2 The script will do the following a When the script starts it checks for the a current version of JAVA previously installed on the system If it is installed its version will be displayed on the screen If it is not installed or there is a version older than 1 4 1 the script will install the newer version b The current version of ImageJ is copied to the directory opt ImageJ_OLD McSwiggen amp Associates JEOL Raw File Opener Plugin Manual Solaris version 2 ImgJOO1 S c The new version is installed into opt ImageJ d Anew menu item is added to the Utility menu of the JEOL EPMA software EPMA gt gt Initialize gt gt Soft Config gt gt Util Menu The ImageJ menu item will be in the format T ImageJ usr local bin ImageJ sh 2 e Reboot the workstation
4. the Analyze gt gt Tools gt gt Scale Bar menu option Add Image Source This option will add a two character field to the scale bar indicating which element or electron signal is being displayed in the image JPEG output This option allows the user to save the images in a JPEG format 16 bit TIFF This option allows the user to save the images in a 16 bit TIFF format instead of the 8 bit default format This option should be used with caution as many imaging programs cannot handle 16 bit TIFF images Note The JPEG output and 16 bit TIFF options are mutually exclusive Directory Selection Window Once the user clicks OK in the Main window the directory selection window will open Figure 2 From this window the user can choose the directory in which the desired maps are to be stored The initial pointer location is to the users home directory In the case of a Solaris system where ImageJ is running on the microprobe computer the user finds and then selects the group and sample of interest When the user has highlighted the sample of interest McSwiggen amp Associates containing the images they can then click on the Select button Select Map Directory xj Lookin C My Documents ca Bo C Adobe J Security CI My Albums CI My Dvds CI My eBooks CI My Music CI My Pictures CI My Videos File Name Cibocuments and SetingstAdministratornay Documents Files of Type All Files
5. EG images to a user specified location in a batch process ImageJ formerly called Image J indicating the Java version is an image analysis and processing program written by Dr Wayne Rasband at the National Institute of Health NIH It is a very popular image processing program that has been greatly strengthened by the support of its user community who have written add on programs plugins that have significantly expanded the software s functionality The fact that it is a native Java program means that it can be compiled and run unmodified on any platform that has a Java SDK installed including Windows MacOS Solaris and Linux McSwiggen amp Associates JEOL Raw File Opener Plugin Manual Solaris version 1 ImgJ001 S The plugin JEOL Raw File Opener has been compiled and is available for both the Windows and Sun Solaris computers Presently it will not run on Macintosh computers According to ImageJ developers Java version 1 4 1 for the Macintosh systems contains bugs and they do not recommend its use Think twice before intalling the Java 1 4 1 update from Apple It is so buggy that ImageJ when run from the command line or by double clicking ij jar is almost unusable http rsb info nih gov ij docs install osx html However version 1 4 1 is required for the operation of the JEOL Raw File Opener plugin Therefore until these problems are corrected a Macintosh version will not be available
6. e collected at one stage position By OK Cancel Heip default they will open directly into ImageJ The user can then work with the images in ImageJ before saving them in their desired format Figure 1 Main plugin window If in addition the Autosave ImageJ files box is checked then the files will also be automatically saved as a 8 bit TIFF unless specified differently below into the same directory location as the original raw image files Bulk Raw File Conversion By selecting this option the user is choosing to convert all of the image files contained within a JEOL sample to either a TIFF or JPEG format In this case the files are not opened into ImageJ but are converted and stored directly to a directory location specified by the user McSwiggen amp Associates JEOL Raw File Opener Plugin Manual Solaris version 4 ImgJ001 S Options Panel The Options panel allows the user to specify what format they would like the images saved as whether to include a scale marker and whether to label the map with an element identifier Add Scale This check box will cause a scale bar to be added to the image When this option is selected the Scalebar Options panel is enabled allowing the user to select the location and color of the scale bar Even if this option is not selected the image is still spatially calibrated so that measurements can be preformed by ImageJ and a scale bar can be added later in ImageJ using
7. ntiguous selections and CTRL click allows for multiple noncontiguous selection McSwiggen amp Associates JEOL Raw File Opener Plugin Manual Solaris version ImgJ001 S Other ImageJ Features LUT Import Color can be added to any map simply by going to the Image gt gt Lookup Tables menu item and selecting a desired color scheme However none of these available color schemes are similar to the JEOL color scheme The JEOL color scheme can be imported by going to File gt gt Import gt gt LUT A window will open that will allow the user to find the look up table of interest The JEOL color scheme is located in the file called JEOLColor txt in the directory ImageJ LUT_Fldr Troubleshooting 1 This program cannot currently open compressed Z files The ImageJ plugin cannot presently open compressed files neither can Photoshop or most other image processing program If your image files end in Z they have to be uncompressed prior to attempting to open Open the File Manager and find the image file you are trying to open To uncompress it just double click on the file A window will open wait a while and then close the window This is all it takes to uncompress these files However you have to do it to each and every file you are going to open It would be better not to compress the files in the first place To stop the EPMA program from compressing the files in the first place do the following On a 8900 1 Go to
8. the directory users epma conf soft On a 8200 1 Go to the directory opt epma conf soft 2 Find the file called icon_compress 3 Change its name to icon_compress NOT If you make this change then all future files will not be compressed McSwiggen amp Associates JEOL Raw File Opener Plugin Manual Solaris version 7 ImgJ001 S
9. to complete the installation ee 99 6 After installation select q for quit 7 Update the EPMA menu gt Go to the Configure menu at the top of the Main EPMA menu gt Select gt Configure gt gt Update menu Run ImageJ To run ImageJ go to the Main EPMA menu and select Utility gt gt ImageJ McSwiggen amp Associates JEOL Raw File Opener Plugin Manual Solaris version 3 ImgJO01 S Operation Manual The plugin can be launched from the ImageJ program either from the Plugins menu or from the File gt gt Import menu Select JEOL Map File Opener The first window that opens Figure 1 allows the user to determine how the map conversions take place and in what format they will be saved Plugin Main Window JEOL Map File Plugin 1 0 F x Mode Panel e 1 F a E i ESSATEN fal j 1 i y Wer A y Hb fin ly SE ph i it i i 7 2 i Y 1 e F S r N Please Select Options The Mode panel allows the user to specify whether they want to open or convert just a single set of maps all of those maps collected at ee a single stage position or whether Open Face in mage Bulk Raw File Conversion they would like to convert all of the Autosave image files maps stored within a JEOL sample Options di rec to ry 5 Add Scale Add Image Source JPEG output 16 bit TIFFS Open Files in ImageJ By i alia selecting this option the user is choosing to open the files that wer
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