Sylvius4 User Manual

Sylvius4 provides a unique computer-based learning environment for exploring and understanding the structure of the human central nervous system. It is available for separate purchase at www.sylvius.com. Alternatively, those who have purchased the textbook (Neuroscience, 5th ed., by Purves, et al, Sinauer Associates, Inc) can obtain a download code by scratching off the box on the cover page. Once the code is obtained, go to http://www.sinauer.com/sylvius4 and follow the instructions to download and register the program.

Features

Sylvius4 features fully annotated surface views of the human brain, as well as interactive tools for dissecting the central nervous system and viewing fully annotated cross-sections of preserved specimens and living subjects imaged by magnetic resonance. This expanded and reconfigured Sylvius is more than a conventional atlas; it incorporates a comprehensive, visually-rich, searchable database of more than 500 neuroanatomical terms that are concisely defined and visualized in photographs, magnetic resonance images and illustrations from Neuroscience, 4th Edition (Sinauer Associates, Inc.; ISBN 978-0-87893-697-7). For users familiar with its predecessors, this version of Sylvius unites the atlas content and utility of SylviusPro (and earlier versions of Sylvius) with the reference content of SylviusVG (and Sylvius for Neuroscience), making this version of Sylvius a single source for understanding the organization of the human central nervous system.

Surface Anatomy provides a visual introduction to the location and names of the major external features and subdivisions of the human brain and includes the following atlases:

Photographic Atlas: Digitally enhanced photographic images of a human brain specimen.

Magnetic resonance image atlas: High resolution 3D reconstructions of a human brain specimen illustrating major surface features.

Brainstem Model: 3D views of a widely used model illustrating the surface features of the brainstem as well as the location of cranial nerve nuclei.

Sectional Anatomy allows the user to explore the internal organization of the brain and includes the following atlases:

Photographic Atlas: Allows users to "virtually dissect" a human brain specimen in the three standard planes (coronal, axial, and sagittal).

Magnetic resonance image atlas: High resolution in vivo atlas comprising coronal, axial, and sagittal sections obtained using T1 imaging techniques.

Brainstem and Spinal Cord: A cross sectional histological atlas of the human brainstem and spinal cord allows users to examine major tracts and nuclei.

Pathways allows users to follow the flow of information in several long-tract pathways of the central nervous system.

Visual Glossary provides users with a searchable glossary providing visual representations, concise anatomical and functional definitions, and audio pronunciation of neuroanatomical structures.

System Requirements and Recommendations

Microsoft Windows: Mac OS X: Mac OS 9:
XP, 2000, NT 4 OS X 10.2 or higher OS 9.2
128 MB RAM 128 MB RAM 128 MB RAM
500 Mhz processor 500 Mhz processor 500 Mhz processor
1028x764 resolution 1028x764 resolution 1028x764 resolution
sound card    

In addition, an internet connection is required to share notes and download product updates.

 

Using the Atlas Launcher

When Sylvius4 is launched, you will first see a "site map" of Sylvius4 content—that is, a complete list of atlas filters available for viewing. Select an entry from the list to load it. Subsequent navigation is performed via the tabs in the upper left corner of the application, or you can click the Show Atlas Launcher button in the upper right corner to re-open the site map.

 

Registration

The first time you run Sylvius4, you will be prompted to register. Registration requires an internet connection. Registering entitles you to product updates and web support. You may enter your full name (e.g., S. Mark Williams) or a nickname (e.g., Maceo). Your email address will serve as your login name to access protected areas of the Sylvius website (www.sylvius.com). It will also be used to send you your password should you forget it. Your email address will not be used for commercial purposes. Registration is not required to use Sylvius4, although it is necessary to access product updates.

 

Using Palettes

Anyone who has used Adobe Photoshop or other palette-based applications will immediately be at home interacting with Sylvius4. Use the tabs to select an atlas class (Surface, Sectional, Pathways). Beneath the tabs, a horizontal list of available atlases appears. Selecting an atlas reveals the Library palette. The Library palette has two columns. The left column lists folders; the right, atlas filters. A filter is a mechanism for categorizing the numerous structures and images in a given atlas. A filter is a similar but more advanced version of a structure mode found in Sylvius 2.0. Sylvius4 will automatically select the core filter list the contents in the right column. The contents of the right column, as noted above, are atlas filters.

Clicking on a filter will load that configuration. Click and hold the title bar of the palette to drag it around the work area. Double-click the title bar or click the minimize icon in the upper right-hand corner to hide the palette contents and show only the title bar. Double-clicking the title bar when the palette is minimized will restore the palette (show its contents).

Most palettes can also be resized. If the palette is resizable, three short diagonal lines will be present in the lower right-hand corner of the palette. To resize, click and drag the lower right-hand corner. Note that, for some palettes, there are limits to the maximum or minimum widths or heights.

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Tool Tips

Throughout the application, tool tips provide a quick and convenient way to get more information about an item‟s properties, behaviors, or actions. A tool tip appears almost immediately when you roll over an object that has a tool tip defined. For example, rolling over the speaker icon in the Structures palette will activate a tool tip that reads "Audio pronunciation."

 

Common Features
As noted previously, Sylvius4 is arranged into atlas classes. Each atlas class has one or more atlases. Each atlas has one or more filters (configurations) for how to view its content.

All atlases use the Structures palette, which lists the structures present in the structure mode. Since not all images in the atlas contain all the structures listed, some structures will appear grayed-out and will not be selectable when the image palette containing that image has the focus (is in the foreground).

Most atlases also use a Navigator palette. In its simplest form, this is just a scrollable field of thumbnails of the images defined in the filter. Clicking on a thumbnail will load that image into an image palette. Clicking and holding a thumbnail image will reveal an options menu. For example, the option Open Image in New Window will load the selected image into a new image palette instead of into the currently focused image palette.

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When multiple image palettes are open, toggling between them updates the Navigator and Structures palettes—the title of the Structures palette changes, its list of active structures gets updated, and the selected thumbnail in the Navigator changes.

Selecting a structure in an image palette or in the list of structures in the Structures palette highlights all instances of that structure in all image palettes and thumbnails in the Navigator, for quick and easy identification.

Interactive features

Audio pronunciation:
Hear the name of the currently selected structure pronounced (currently in English only).

Notes:
The Notes palette allows the user to save any comments about an atlas filter. Notes are stored locally on the user‟s computer. See A Notes Primer on the page 6 for more information.

Palette interface:
Open multiple image palettes; view multiple images at the same time.

Orientation:
See an image showing the orientation of the selected brain view relative to the cranium and the body.

Quiz mode:
When rolling over a structure, tool tips read "Press "A‟ key for answer." Pressing the "A" key will reveal the name of the structure.

Structure visibility toggle:
Hide or show the structure highlighting on the images.

Hierarchical structure grouping:
Structures in Sylvius4 are hierarchically grouped to illustrate, for example, the full extent of a pathway. When a structure is part of a group, the Toggle Grouping button in the Structures palette becomes enabled. Use this button to jump between viewing the entire grouping and structures that comprise the group.

Fit-to-Width:
If enabled, the image will automatically scale to fit the width of the palette as the palette is resized. When fit-to-width is disabled and scrollbars are visible, press the spacebar while clicking to drag the image in the scroll pane area.

Zoom to…:
Scales the selected image to 100%, 150%, or 200%.

Image mark-up tools:
Draw tools allow you to annotate an image using a pencil/freehand tool and a line/arrow tool.

Customize:
Users have control of how Sylvius4 starts-up, how the program presents colors over brain structures, whether audio pronunciations play automatically or not, how windows open and fade, and when the program checks for updates. To alter any one of these aspects of Syvlius4, click on the Preferences tool icon (hammer and wrench) in the top right pane. Select the feature you wish to change and alter the settings accordingly.

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Printing:
Print images and accompanying term and notes information by clicking the Print button in the upper-right corner. You will see a preview of the printout. Follow the prompts to print the image and associated text.

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A Notes Primer
Notes are a powerful feature that you can use to annotate atlas filters. Notes are stored locally on your computer. Note that content saved locally is not dependent on the location of the Sylvius4 application. Launch the Notes palette by clicking the Notes button in the upper right corner of the application. To add a note, click the Add Note button in the palette. The notes interface will enter edit mode. After typing the note, click off of the notes area to quit edit mode. To modify a note, click on its entry to enter edit mode and make any updates. If you would like to remove a note, clear its contents while in edit mode.

 

Features by Atlas

Surface Anatomy Atlas

MR Atlas
The surface MR atlas contains a 3D reconstruction of the surface of a human brain specimen derived from T1-weighted magnetic resonance images. The red dots serve to mark the location of an identified structure. The user can examine the specimen from multiple viewpoints by selecting thumbnails in the Navigator palette. Selecting Interactive MR rotation in Atlas Extras button in the Navigator palette allows the user to view the specimen from over 125 unique
angles.

Photographic Atlas
The surface photographic atlas contains photographs of the surface of the brain from different perspectives. Lightly colored areas mark the location, shape, and size of structures.

Brainstem Model
This module comprises images of dorsal and ventral views of a rubber brainstem model illustrating the topography of surface features of the brainstem and the locations of cranial nerves and cranial nerve nuclei. Lightly colored areas mark the location, shape, and size of structures.

Sectional Anatomy Atlas

MR Atlas
The sectional MR atlas contains T1-weighted magnetic resonance images (coronal, axial, and sagittal) of a single human subject. The dots serve to mark the location of prominent structures.

The Navigator palette for this atlas uses a 3D selector tool, allowing the user to choose images for detailed viewing while providing a convenient way to view the orientation of the images. Switching the focus among open image windows updates both the thumbnails and the 3D
selector.

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Photographic Atlas
The sectional photographic atlas comprises images of a single human brain specimen that was sectioned and photographed in the three standard planes (coronal, axial, and sagittal).

The Navigator palette for this atlas uses a 3D selector tool allowing the user to choose images for detailed viewing while providing a convenient way to view the orientation of the images. Switching the focus among open image windows updates both the thumbnails and the 3D
selector.

Selecting 3D reconstruction in the Atlas Extras button in the Navigator palette allows the user to view virtual dissections of this specimen. Also, users can toggle between the en face and 3/4 views of a section by selected the Show orientation button in the Navigator palette.

Brainstem Cross Sectional Atlas
This atlas contains transverse sections of the brainstem and spinal cord. The images were acquired and processed to simulate myelin staining; thus, white matter appears darker, and gray matter lighter. Lightly colored areas mark the location, shape, and size of structures.

In addition to the thumbnails, the Navigator palette for this atlas uses two images to view the location of the sections at a glance. Use the sliders alongside these orientation images to quickly select sections to examine in detail. Switching the focus among open image windows updates both the thumbnails and the sliders.

Pathways Atlas

Animated Pathways
The animated pathways atlas allows you to view the flow of information between the structures comprising selected major long tract pathways of the central nervous system. Use the Play/Pause and Rewind buttons to control the neural impulse traveling along the pathway. Click on a structure name to show its description. Be sure to have the computer‟s sound ON to hear audio emphasis of synaptic transmission.

 

Visual Glossary

Overview

Sylvius4 contains a special reference module called Visual Glossary (available as a separate application called, SylviusVG: A Visual Glossary of Human Neuroanatomy). The Visual Glossary is an interactive glossary of the human central nervous system, featuring over 500 neuroanatomical structures and terms, each including a definition, one or more high resolution images, illustrations (from Neuroscience, 4th Edition, Sinauer Associates, Inc.; ISBN 978-0-87893-697-7) or animations, audio pronunciation, and links to related terms and structures also found in the glossary. The interactive features within the Visual Glossary enable efficient navigation, study, review, and user-
defined annotation:

  • Glossary content is fully searchable and cross-referenced
  • The Browse by Category feature allows the user to view structures and terms relevant to predefined topics
  • Recently viewed images can be quickly reviewed via the History function
  • Structures and images of interest can be bookmarked
  • High resolution images and animations can be magnified 200%
  • Term descriptions can be annotated via powerful Notes feature
  • Quiz mode allows for testing on structure identification
  • Printing allows users to create a hardcopy version of any glossary entry complete with image, description, and user-defined notes

Getting Acquainted

After the registration prompt, the main interface will load. The left side of the window contains interface elements related to navigating glossary content, while elements on the right side apply to the currently selected term.

In the upper left-hand corner of the window, there are three tabs: Index, Bookmarks, and History. Changing the selected tab updates the contents of the terms list directly below the tabs. The Index listing contains all of the terms included in Sylvius4. The History maintains a list of the last 25 viewed images. Any structures bookmarked will be included in the Bookmarks listing. Use the text input field next to the three tabs to search through the terms in the list.

Below the terms list is a list of categories. Selecting a category filters the terms list to include only those assigned to the category. For example, choosing the category "Visual system" will display all the glossary terms related to neuroanatomical components of the visual system.

To the right of the lists are interface elements related to the currently selected term. The definition of the term is displayed below the image viewing area. The Notes tool is located to the right of the definition and is used to view and manage your notes about the structure you are currently viewing. Notes anagement
buttons are located below the Notes field. Use them to add, save, and delete your notes.

To the right of the main image is the image toolbar. Use the buttons in the toolbar to interact with the currently selected image; for example, to magnify the image, to toggle its labels on and off, or to hear a term pronounced. If you are unsure of a button‟s action, you can pause for a moment with the mouse
over a button to activate the button‟s tool tip. Tool tips provide a convenient way to get more information about a button‟s function. Tool tips that end in "…" signify that clicking the button will display additional prompts.

The Visual Glossary window can be resized to provide more space for the interface elements. As the size increases, the window elements will resize. Although the window can be made smaller than its initial size, the content will be cropped.

Interactive features

History:
The last 25 terms viewed are remembered. Select the History tab or use the Forward and Back buttons on the far right to navigate the history.

Bookmarks:
Terms and images can be bookmarked for later use or study. Click the Bookmark button on the far right to add the selected term. If the selected term contains multiple images or animations, the selected image will also be bookmarked. Returning to the term via the bookmarks listing will load the image selected when the term was bookmarked. If the selected term is already bookmarked, the Bookmark button will change to show the "remove bookmark" icon. Clicking the button will remove the selected term from the bookmarks. Bookmarks are saved locally on your computer. Note that content saved locally is not dependent on the location of the Sylvius4 application.

Search:
The search feature allows for efficient navigation of Visual Glossary content. The search input field is located next to the three tabs in the upper left-hand corner of the window. If the query is found in the term name, its description, or your notes about the term, the term will appear in the list. For example, searching for "stria" will return, among other terms, "striatum", "stria medullaris" and "cuneus" (the cuneus contains the "striate" visual cortex, which is returned in this particular search). As you type, the search results list will be updated. To further refine your results, continue typing. The content is filtered while typing, so pressing the Enter or Return key is not necessary. Clear the search field to remove filtering on the terms list. When switching between tabs, the search field is cleared.

Multiple Image Support:
Each term in the glossary contains up to four high resolution images and animations. If more than one image is available for the selected term, a "drawer" will appear at the bottom left of the image viewing area containing numbered thumbnails of all the images available. You can click the tab on the right edge of the drawer to show and hide it. Clicking on a thumbnail will load that image into the image viewing area. In addition to the definition supplied with the term, an individual image may also contain a description relevant to that specific image. If present, it will be displayed below the main description with an "About this Image" heading.

Animation Support:
When an animation is loaded into the image viewing area, a playback controller will appear in the upper left-hand corner. There are two buttons in the controller: play/pause and rewind. Use the controller to interact with the animation. In the Interactive MR Rotation window (Atlas extra in Surface Anatomy MR Atlas), four buttons appear: play/pause, step back, step forward, and orientation. Again, use these buttons to interact with the animation and view the surface of the brain from many different perspectives.

Quiz:
The Visual Glossary contains a self-quiz feature. Clicking the Quiz button on the right side of the window will enable quiz mode, hiding the terms list, description, notes field, and image labels. The quiz toolbar will appear with buttons for navigating through the terms, as well as a button to show and hide the description and notes fields. The terms in the currently selected category will be presented in a random order. Clicking the Quiz button again will exit quiz mode. Selecting the Bookmarks or History tabs will also turn off quiz mode.

Printing:
The print feature in the Visual Glossary allows the user to create a hardcopy version of the selected term. The print-out includes the term name, its description, your notes, and the image. Clicking the Print button will launch the printer setup prompts.

Magnify:
Clicking the Magnify button will zoom the image to 200%. Clicking the Magnify button again will return the image to standard magnification. Magnification works particularly well in full screen mode (click the Full Screen button to toggle in and out of full screen mode). Some images are low resolution and cannot be magnified.

Audio Pronunciation:
Click the Speaker button to hear the pronunciation of the selected term.

Notes:
Just as in the main Sylvius4 window, Notes are a helpful feature you can use to make annotations to the provided term descriptions. Since notes are stored locally on your computer, when you create your first note you will be prompted to allocate storage space. Note that content saved locally is not dependent on the location of the Sylvius application. The notes tool is located to the right of the term description field. To add a note, click the Add Note button. The notes interface will enter edit mode. After typing the note, click off of the notes area to quit edit mode. To modify a note, click on its entry to enter edit mode and make any updates. If you would like to remove a note, clear its contents while in edit mode. You can also clear all of the notes for the selected term or all notes for all terms by clicking the Clear Notes button. This will display a prompt asking what action to perform.

 

When the Updates button in the upper right corner is highlighted, this means that updates to Sylvius4 are available. Clicking this button will open your web browser and take you to the Sylvius4 website, where you will be able to get more information about nature of the update. Although only registered users have access to updates, all users will be notified of their availability. To check manually for updates, open the Preferences palette and select Software Update.

 

Q: Can I keep my notes when I update Sylvius4?
A: Yes. Notes are stored in a separate location on your hard drive, independent of the location of your Sylvius4 application.


Q: Do I need an internet connection to run Sylvius4?
A: No. However, one is required in order to acquire the application using the download code, to register the application, and to get product updates.

Q: How much space should I allocate for notes?
A: We recommend 1 MB to avoid being prompted to increase the allocation in the future.

 

Issue: I cannot register.
Solution: First, make sure you are connected to the internet. Next, check that the Sylvius.com website is available. Next, check that you‟ve satisfied the registration requirements:

Name. The name you specify should be at least 4 characters long and no more than 40. Please refrain from using angle brackets and quotation marks.

Password. Your password should be at least 4 characters long and no more than 20. Only alphanumeric characters, hyphens, and exclamation points are permitted.

After you are registered, you may use Sylvius4 anywhere, regardless of whether have an active internet connection. In some cases, it may possible to register using a VPN client or HTTP proxy server. Unfortunately, we can't guarantee that all remote connection configurations will be compatible with the Sylvius4 registration process and apologize for the inconvenience.

Please include the specific error message(s) received if you contact Sinauer Assoc., Inc.'s help account.

If this problem persists or if any other problem arises, please contact support@sinauer.com and include the name and version of your web browser. Additional support is available at http://www.sylvius.com/.

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Updated 12/31/11 - Velkey