AT L A S N A V I G AT O R User Manual
Contents
1. on Click on List Structures to open a window displaying all of the structures in the selected atlas USER MANUAL Structures Structures of Mouse CO7BL 6 Nissl Coronal plates 415 dopaminergic group 413 Aad anterior amygdaloid area AC nucleus of the anterior commissure ACB nucleus accumbens ACEo nucleus accumbens core ACBs nucleus accumbens shell ACd anterior cingulate cortex dorsal part ACY anterior cingulate cortex ventral part AD anterodorsal nucleus of the thalamus ADP anterodorsal preoptic nucleus AHA anterior hypothalamic area AHN anterior hypothalamic nuc leus AHMa anterior hypothalamic nucleus anterior part AHA anterior hypothalamic nucleus central part Ald agranular insular cortex dorsal part Alp agranular insular cortex posterior part Aly agranular insular cortex ventral part AM anterornedial nucleus of the thalamus AME nucleus ambiguus AMHA amygdalohippocampal area After an atlas has been selected all of the plates for that atlas are displayed in the scrolling list field near the middle of the Atlases Window Mouse 129 Sv Myelin Coronal plates Mouse 129 Sy Nissl Coronal plates Mouse CSTEL 6 Myelin Coronal plates Clicking on a plate will enable the Select button and display a thumbnail if available on the lower part of the window USER MANUAL Mouse 123 5 Myelin Coronal plates Mouse 12375 Nissl Coro2. windows 95 r If you are using Microsoft Windows select the version of the Windows operating system CPU Type Pentium 8 Also if using Microsoft Windows select the CPU that you are using Enter in your email address This will be the address to whom replies will be sent Enter in a summary of the support you need Enter in a description of the technical support with as much detail as possible in the last field Click on Send to send the technical support request or Cancel to dismiss the window without sending it You must be on the Internet for this request to be sent properly Please refer to the operating system manual of your computer to set up connectivity to the Internet The Bug Report Window Any software bugs that you find may be reported to us using the Bug Report Window You can open this window by selecting Bug Report from the Help menu of the menubar USER MANUAL Bug Report Bug Report Environment Description Cancel Enter in a summary of the bug report Enter in your email address This will be the address to whom replies may be sent if necessary The center part of the window is used to profile the product and the environment The Product tab opens first Version ie als all Aaa Valea amp filled in automatically when you open this window You do not normally have to change this value LJ Workaround If
3. Atlas Navigator exe new on Microsoft Windows Message The original application has not been Changed The new one is named Atlas Mavigator new If you click on OK to quit the current application and launch the new one any windows currently displaying plate sections will be closed A new instance of Atlas Navigator will be launched from the beginning Under Microsoft windows there is also a DOS window that will opened briefly that controls the application switching It will close automatically when the process control switches to the newly updated application 24 USER MANUAL The Preferences Window The preference window is opened by selecting Preferences from the Edit menu of the menubar Preferences O Open Atlas Palette with Mew window O Launch Copy Outline with Image O Show Tips at Startup These preferences are recorded and persist for all future uses of Atlas Navigator on your computer Check or uncheck each preference as is needed LJ Open Atlas Palette with New Window Open the Atlases Window whenever a new Atlas Navigator Window is opened LJ Launch Copy Outline with Image When launching or copying the outline file include the image in the background of the line art LJ Show Tips at Startup When starting Atlas Navigator show the Tips Window e i Click on Accept to store these preferences Click on Cancel to cancel any changes Other Inter
4. 11 USER MANUAL K PREVIOUS FAST The double left arrow is used to quickly move through all previous plates of the series When the first one is reached the display stops Press and hold the mouse button on this navigational button When the mouse button is released the changing display will stop NEXT FAST The double right arrow is used to quickly move through all next plates of the series When the last one is reached the display stops Press and hold the mouse button on this navigational button When the mouse button is released the changing display will stop Under the Windows operating system using the Previous Fast or the Previous Next buttons does not properly display the plate sections as they are being quickly moved back and forth However this does display properly on an Apple Macintosh Source File Controls The buttons on the center control the copying and launching of the original files from the CD ROM Copy Outline Launch Outline Copy Image Copy Outline is used to copy the original source data file containing the line art from the CD ROM for the atlas plate section displayed on the current Atlas Navigator window to a local folder Copy Image Copy Image is used to copy the original source data file containing the image from the CD ROM for the atlas plate section displayed on the current Atlas Navigator window to a local folder Both copy procedures will search the mounted CD RO
5. Window to open the next time you start Atlas Navigator uncheck the box in the window all Click on Next Tip to see the next tip 17 USER MANUAL Click on Previous Tip to see the previous tip Click on Close to dismiss the window The Technical Support Window You can get limited technical support on Atlas Navigator by using the Technical Support Window Open this by selecting Technical Support from the Help menu of the menubar Technical Support Technical Support Technical Support is given by email only to registered users You must have a valid registration number and you must have sent in the registration information Please summarize your request below and write a more detailed description of what you need below Software Info Mac 05 Version CPU Type Win OS Version Windows 95 CPU Type Pentium 4 Tech Support Info Cancel The window has fields that you need to fill out and choices to make to give us as much information as possible as your operating environment and the support that you need Version a om A Sige filled in automatically when you open this window You do not normally have to change this value ae DEzLeR ID I If you are usinga Macintosh enter in the version of the operating system l e 8 5 8 6 9 0 9 0 4 OS X 18 USER MANUAL CPU Type Power PC Also if on a Macintosh select the CPU that you are using in O5 Version
6. windows File Edit Internet Window Help 9 07 AM Fe 2 Atlas Navigator Cj Atlases ii Did you know You can disable the display of the Tips window by setting the preferences for it to off or by unchecking the checkbox below C show Tips at Startup Copy Outline Launch Outline Store Cer JO Sync Seet To Displays LE File Edit Internet Window Help Atlas Navigator Mouse 129 5 Myelin Coronal Mouse 129 S Nissl Coronal pl Mouse C57BL 6 Myelin Corona Mouse C57BL 6 Nissl Coronal Tip of the Day Vv Did you know You can disable the display of the Tips Window by setting rl A Fan Ihe checkbox IV Show Tips at Startup INNERN Close 44 al p ali CopyOUTIAe MENRHIGUtiAE Beej esta Sync Copy Image LEERE Select To Display gt Mstart Hy 3 Control Panel Gatias Navigator E Timbuktu pro youn Exchange Files with ait Atlas Navigator Bee 12 02am You will learn more about these windows and others in the next chapter USER MANUAL Platform Differences Atlas Navigator was developed to support both the Apple Macintosh computer and all of the Microsoft Windows operating systems The graphical user interface is for the most part completely similar when running on all of the different computers and operating systems There are minor cosmetic differences that are in part due to incomplete specification of the pro
7. ATLAS NAVIGATOR User Manual YTIG Inc P O Box 721959 San Diego CA 92172 1959 Table of Contents Introduction i INTRODUCTION 1 mh What Do I Need to Run Atlas Navigator Getting Started Launching Atlas Navigator Registration Platform Differences 9 9 aA BO N Using the CD ROMs NAVIGATING CHAPTER 2 The Atlases Window 7 The Atlas Navigator Window 10 The Info Window 14 The Plate Structures Window The Search Window SUPPORT CHAPTER 3 The Tips Window The Technical Support Window The Bug Report Window The Updates Window The Preferences Window Other Internet Resources 14 15 17 18 19 22 26 26 ICON KEY Important Tip Alert M Macintosh W Windows USER MANUAL Introduction and Windows based computer systems It was designed to work with the supplied atlas CD ROM disks from Elsevier Science You do not need to use Atlas Navigator in order to use the files on the CD ROM disks However Atlas Navigator is designed to make it easier to navigate through the many hundreds of files and to offer one click launching of the outline and imaging programs Atlas Navigator also has built into it a database that knows the location of the structures for all of the various plates sections and atlases You can search easily for structures and Atlas Navigator will show which sections contain those structures N tlas Navigator is a software application written for both Apple Macintos
8. M for the correct file If Atlas Navigator cannot locate the correct file an Open File dialog window will open asking you to locate the file Copy Outline is affected by the preference setting for Launch Copy Outline with Image If this preference is on the outline file will contain the image in the background layer will be copied If this preference is off only the line art file will be copied On the Macintosh the creator of these files is Adobe Illustrator 12 USER MANUAL Copy Image copies a TIFF formatted file On the Macintosh the creator of these files is Adobe Photoshop If you don t have Photoshop it can be opened by any TIFF capable graphics program Launch Outline Launch Outline is used to launch the associated outline software program typically Adobe Illustrator and to open in it the line art of the atlas section plate displayed in the current Atlas Navigator window Launch Image is used to launch the associated imaging software program typically Adobe Photoshop and to open in it the image of the atlas section plate displayed in the current Atlas Navigator window Note that if Illustrator or Photoshop is currently running on your computer launching the outline or image may not bring that window to the front of other windows If so use the Application Menu on the Macintosh or the Task Bar on Windows to bring the window to the foreground Plate Memory Controls The buttons on th
9. e right side control the storage of the currently displayed plate into disk memory for later recall by using the pull down menu Click on the Store button to store the currently displayed plate into memory The plate will be available in all Atlas Navigator windows from the pull down menu You may store as many plates as desired Click on the Clear button to clear the currently displayed plate from memory The plate will no longer be available from the pull down menu on the Atlas Navigator windows Select To Display 7 Select from this pulldown menu to one of the stored plates in memory This will display the plate in the current Atlas Navigator window 13 USER MANUAL LJ syne If the Sync button is checked in this and any other Atlas Navigator window these plates will be changed together in synchrony when the navigation buttons are used This is useful when similar planes of section are in atlases displayed in separate Atlas Navigator windows and you want to examine the correponding sets of plates simultaneously Info Window If an Atlas Navigator window is displayed information on the atlas can be displayed by selecting Get Info from the Window menu Information Atlas Mouse CS7BL 6 Nissl Coronal plates Animal 9 Species Mouse Strain CS7BL 6 Stain Nissl Plane Coronal Render Micrograph Plate 0460 Eregma 1 30 mm Publication Comparati
10. et up connectivity to the Internet None of your operating system files will be altered Only the files that are used by Atlas Navigator will be updated Cancel Click on Cancel before updating to dismiss the window without performing an update or click on it while updating to cancel any impending updates b Click on this arrow to expand the window downward to see more information on the update process Click on it a second time to collapse the information 23 USER MANUAL Updates Click on Update Now button to check for new and updated versions of the software and databases Ej Update Executable e Update Data Files F When the update process has concluded a log is written to the folder named Install Logs inside the Data folder If there are problems you can copy and paste this log to a Technical Support report If the executables are being updated you will be asked to restart Atlas Navigator after the updating has concluded Under Microsoft Windows the old application is renamed to Atlas Navigator exe bak Click OK to quit the current application and launch the new one Old application Will be renamed to Atlas Navigator bak If you click on Cancel the following dialog appears The original application will not have been changed However the new one that has been downloaded will be saved into the same folder as Atlas Navigator and named Atlas Navigator new on the Macintosh and
11. everity Reproducibility Always Reproducibility Select from this menu the reproducibility of the bug Enter in a full description of how to reproduce the bug in the field below this menu Be as accurate as possible If you don t know how to reproduce it say so Click on Send to send the bug report or Cancel to dismiss the window without sending it You must be on the Internet for this bug report to be sent properly Please refer to the operating system manual of your computer to set up connectivity to the Internet The Updates Window Atlas Navigator has the powerful capability of being able to update itself and all of the data files by accessing update servers over the Internet To open the Updates Window select Check for Updates from the Internet menu of the menubar 22 USER MANUAL Updates Click on Update Now button to check for new and updated versions of the software and databases Update Executable e Update Data Files b Bi Update Executable Lyf Update Data Files You may choose to update just the executables which is the software program Atlas Navigator itself or the data files Click on Update and Atlas Navigator will locate the server on the Internet compare the files it needs for any updates and retrieve and install them You must be on the Internet for this update server to operate properly Please refer to the operating system manual of your computer to s
12. gramming libraries For example the Windows software will display a gray background on the text of some of the windows None of these will affect the operation of the software For more information see the chapter on Technical Using the CD ROMs The atlas that this software is supplied with comes on several CD ROMs The CD ROMs are ISO 9660 compliant and can be used in both Apple Macintosh and Microsoft Windows computer systems Each CD ROM has a subset or the whole atlas on it Please refer to the documentation that came with the atlas to understand how the files are grouped on each CD ROM Typically the CD ROM containing the animal and type of file are inserted in the CD ROM drive Atlas Navigator will then do its best to locate the needed files from that CD ROM disk when you launch or copy an outline or an art file If Atlas Navigator can not find the file on any mounted CD ROM it will prompt you to locate it You should then eject the current CD ROM and insert the correct disk containing the file that is needed If you have more than one CD ROM drive you can insert more than one CD ROM disk at a time Atlas Navigator will search all of the mounted CD ROMs for the files that it needs USER MANUAL Navigating the CD ROMs until you Copy or Launch a plate section that is displayed in one of its main window More information on Copy and Launch are below in the Atlas Navigator Window section N tlas Navigator uses atlases that a
13. h Atlas Navigator is not meant to substitute for the outline programs that can open all of the lineart that is supplied on each atlas CD ROMs It also does not perform 3D display or analysis circuitry or sophisticated database operations It is designed to simply be the first tool to use to navigate through the atlas files Use Atlas Navigator to locate the plates you want to use and then run other software applications to do mote critical display or analysis What Do I Need to Run Atlas Navigator Atlas Navigator runs on all Apple Macintosh and Windows based computers running Windows 95 Windows 98 Windows NT and Windows 2000 A minimum of a total of 32 64 MB of overall system RAM is recommanded for the computer 5 MB of free memory is recommended for Macintosh computers While Atlas Navigator itself does not require a CD ROM drive when operating the installation software and atlas data files are supplied on CD ROMs The total size of the files are very large and it is recommended to leave the data files on the CD ROM when using Atlas Navigator Atlas Navigator will automatically locate the needed files on the CD ROM and alert you if it cannot find them There are no special requirements for video cards The images are best displayed in thousands or millions of colors on the Macintosh and high or true color on the Microsoft Windows computers USER MANUAL To perform software and data file updating an Internet connec
14. igator windows are opened clicking on each one to bring it up as the frontmost window will update the information in the Plate Structures Window Click on the Copy button to copy selected data from the window into the clipboard Click on the Done button to dismiss the window Search Window If an Atlas Navigator window is displayed the structures in all of the atlases can be seatched by selecting Search from the Window menu Structure to Search Select Structure gt ME Name m Abbrewiation O Exact Match 15 USER MANUAL structure to Search The top field accepts a string This is matched against either the name or the abbreviation of the structure is Marne Abbrev lation Select Name or Abbreviation by clicking on the radio button Select Structure Instead of typing the structure search string the pull down menu can also be used The items in the pull down menu will change depending on whether the Name of the Abbrevation is selected Exact Match If the Exact Match checkbox is checked then the structure name or abbreviation must match exactly the string in the field Search er Click Search to start the search When the search completes all of the atlases and the plates that contain this structure are displayed in the bottom scrolling list field Structure to Search corpus callosum corpus callosum Search i Mame m Abbrewiation Exact Ma
15. ke Double click the folder to open it You will see the following files Edit View Favorites Tools Help H Back mb search C Folders Documenta Atlases Misc 4 objectis 2 31 ME My Computer Launching Atlas Navigator Launch Atlas Navigator by double clicking on it In a few seconds the About Window will open Label j oa Concept and Development L Warren G Young 2000 YTIG Inc All Rights Reserved F O Box 7219593 San Diego Ca 32172 193959 355 484 2672 phone 858 494 3678 fax TIG Inc qo First time run building structure database Atlas Navigator will then build its internal database during this first run It may take a couple of minutes depending on the speed of your computer Please do not interrupt it at this point Once this first run process has completed Atlas Navigator will start up almost instantly on successive launches It will only rebuild itself again when it detects that new atlases were added or if some of the data files have changed You need to be connected to the Internet in order to send this registration information USER MANUAL Registration Once the build process has completed the serial number must be entered into the registration window Enter Registration Number Enter in your registration number without the registration number you can only navigate using thumbnails and screen resolution images but cannot access the full outlines and high
16. nal plates You can use the UP and DOWN arrows on the keyboard to move quickly through the plates Any available thumbnails will display in the window To display the full size image of the plate section either double click on the Plate item or press the Select button The image of the plate will appear in the frontmost Atlas Navigator window Atlas Navigator Window The Atlas Navigator window is the main window of the software application This is where the selected plates of the atlases are displayed 10 USER MANUAL 0460 Mouse CS7BL 6 Nissl Coronal plates ai lt q gt Mouse COTBL 6 Miss Coronal plates Copy Outline Launch Outline L syne 10 49 Plate 0460 Bregma 1 30 mm Launch Image Select To Display You may open several Atlas Navigator windows Many windows may be useful when comparing similar sections from different strains Navigation Controls Once a plate is displayed the controls on the Atlas Navigator window become active The buttons on the left side are the general navigational controls lea fool FIRST The leftmost button is used to move to the first plate of the current atlas LAST The rightmost button is used to move to the last plate of the current atlas PREVIOUS The single left arrow is used to move to the previous plate of the current atlas x amp EI NEXT The single right arrow is used to move to the next plate of the current atlas
17. net Resources Atlas Navigator has links to other Internet resources available from the Internet menu of the menubar As these will change with updates please refer to them by selecting each item and reading the description in each window These will all require a live Internet connection and a Web browser configured for use on your computer 25 26
18. re installed in its database It does not need There is only one main window named Atlas Navigator This window displays the atlas plate section that you select for viewing You may have as many of these windows open as you want To open another window select New Window from the File menu Several other windows may be opened to control the selection searching and display of information of plates These windows are sometimes called floating palette windows because they float above the main windows and their actions affect the current or frontmost main Atlas Navigator window The first palette window that opens when the program starts up is the Atlases Window Atlases Window All of the atlases that have been installed are displayed in the top scrolling field of this window You can toggle this window on and off by selecting the menu item Atlases from the Window menu USER MANUAL Mouse 129 Sy Myelin Coronal plates Mouse 129 Sy Nissl Coronal plates Mouse CS7EL 6 Myelin Coronal plates Mouse CS7EL 6 Nissl Coronal plates List Structures Plate Selecting an atlas highlights the About and List Structures buttons The About button will open a window that shows information about the atlas itself This is typically the front cover of the hardcopy atlas About Atlas Comparative Cytoarchitectonic Atlas of the 129 Sv and C57BL 6 Mouse Brains List Structures
19. resolution images Registration Number Enter the serial number provided with the software If you do not have a serial number click on the Not Yet button This will allow Atlas Navigator to start but you will not be able to launch or copy files from with the program nor will you be able to update the software or data files automatically Once the serial number has been correctly entered the registration information window will open User Information Enter this information to complete the registration If you choose not to complete this registration step you can only use your local copy Mo updating ower the Internet will be allowed required field Mame CC Institute or Company Po Department T Address Po City State or Province Country Zip or Postal Code Phone EMail Address Hot Yet USER MANUAL Until you register your information and click on the Send button you will not be able to update the software and data files automatically Your name institute or company and email address are required Until these fields are entered the Send button is disabled If you click on Not Yet no registration information is sent You can still use Atlas Navigator freely and copy and launch data files but you cannot update the software or the data files over the Internet until the registration information is sent After the registration windows close Atlas Navigator opens its main
20. tch 36 plates found D671 Mouse 129 5 Myelin Coronal pla C460 Mouse 123 5v Missl Coronal plates D450 Mouse 123 5v Missl Coronal plates 0525 Mouse 123 5v Missl Coronal plates 0550 Mouse 125 S Missl Coronal plates 0500 Mouse 125 Sy Missl Coronal plates DEZO Mouse 125 S Missl Coronal plates DEED Mouse 123 5v Missl Coronal plates 0590 Mouse 123 5v Missl Coronal plates OFZO Mouse 125 Sy Missl Coronal plates 0750 Mouse 125 S Missl Coronal plates 0730 Mouse 129 8 Nissl Coronal plates Any plate may be selected for display in the current frontmost Atlas Navigator window by double clicking on the plate or by selecting it and Click on the Show button 16 USER MANUAL Support everal other windows are available for information and support Open each window by choosing the appropriate item from the Window menu in the Menubar The Tips Window If this is the first time running Atlas Navigator the Tips Window opens first You can also open it at any time by selecting Tip of the Day from the Help menu of the menubar Tip of the Day Did you know Atlas Navigator can be used to install your own atlases Eijl Show Tips at Startup The tips contain some valuable information on how to effectively use Atlas Navigator with the data CD ROMs Each time the Tips Window opens a random tip will be displayed LJ Show Tips at Startup qf you don t want the Tips
21. there is a workaround to this bug please check this box Enter the details of the workaround in the description field below dF Severity Crash Select from this menu the severity of the bug Click on the Environment tab to display configuration choices for the environment USER MANUAL Bug Report _ Bug Report Environment Mac OS Yersion I Description Mac 05 Version Win OS Version windows 95 T CPU Type CPU Type Win OS Version Windows 95 zJ CPU Type I If you are using a Macintosh enter in the version of the operating system l e 8 5 8 6 9 0 9 0 4 OS X Also if on a Macintosh select the CPU that you are using If you are using Microsoft Windows select the version of the Windows Operating system Also if using Microsoft Windows select the CPU that you are using The bottom part of the window is used to enter in the description and reproducibility of the bug The Description tab opens first Enter in a full description of the bug in the description field Be as accurate as you can giving additional information where you feel it is needed In order to produce a fix for these bugs we need to understand fully the nature of the problem as well as being able to reproduce it Click on the Reproduce tab to open the fields for the reproducibility aspects USER MANUAL Bug Report Bug Report Environment S
22. tion is required See your manual for your computer and its operating system to ensure that connectivity to the Internet is enabled To see the original source files on the outlines Adobe Illustrator is required The files on the Mouse Atlas database are stored in Illustrator 8 0 format The image files are stored as TIFF files On the Macintosh Adobe Photoshop will be launched to open these files Under Microsoft Windows the program associated with TIF files will open them However any graphics software program capable of displaying TIFF images can be used to open them directly Getting Started Atlas Navigator is supplied separately on its own CD ROM disk Insert the CD ROM into the CD ROM drive For Macintosh Open the volume Application Disk that appears on the desktop Drag and drop the folder named Macintosh Copy To Hard Drive to any desired location on your hard drive You may rename this folder to anything you would like Double click the folder to open it You will see the following files O Macintosh Copy To Hard Drive E E items 5 48 SB available Each Atlas Navigator Documentation In Windows the chasing arrows may not appear when bulding the database USER MANUAL For Windows Open the drive that is assigned to your CD ROM Drag and drop the folder named Windows Copy To Hard Drive to any desired location on your hard drive You may rename this folder to anything you would li
23. ve Cytoarchitectonic Atlas i Publisher Elsevier Scientific Publishers Year 2000 Updated Not Applicable Number of Plates 49 If multiple Atlas Navigator windows are opened clicking on each one to bring it up as the frontmost window will update the information in the Info Window Click on the Copy button to copy the data from the window into the clipboard Click on the Done button to dismiss the window Plate Structures Window If an Atlas Navigator window is displayed all of the structures in the currently displayed plate can be displayed by selecting Get Plate Structures from the Window menu 14 USER MANUAL 33 structures ACBe nucleus accumbens core ACES gt nucleus accumbens shell ACd anterior cingulate cortex dorsal part Ald agranular insular cortex dorsal part lv agranular insular cortex ventral part aco anterior commissure olfactory limb CLA claustrum CF caudate putamen DP dorsal peduncular area EPd endopir iform nucleus dorsal part ec external capsule fa corpus callosum anterior forceps GU gustatory cortex IL infralimbic area ISL insula of Calle ja SLM insula of Calle ja major LSd lateral septum nucleus dorsal part LSi lateral septum nucleus intermediate part lot lateral olfactory tract conv Mouse CSTBL 6 Nissl Coronal plates Oy Plate 0460 Eregma 1 40 mm If multiple Atlas Nav
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