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h1. ALLEN Human Brain Atlas

This is the online help for the Human Brain Atlas web application.






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h2. The Data Set

The Allen Human Brain Atlas consists of two primary sources of gene expression data:        microarray numerical value data and _in situ_ hybridization (ISH) 	  image data.

For complete details please see the [Microarray Platform Selection|http://human.brain-map.org/content/MicroarrayPlatformSelection.pdf?1307563382], [Whole Brain Microarray|http://human.brain-map.org/content/WholeBrainMicroarray_WhitePaper_March2011.pdf?1307563370] and [In SituHybridization|http://human.brain-map.org/content/ISHOverview.pdf?1307563360] white papers on our [Documentation|http://human.brain-map.org/docs.html] page.

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h2. Supported Platforms

This application has been tested  with the following configurations.           You may notice  irregularities with software that has not been tested.           There  are known issues when viewing heat map data using unsupported browsers.
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|| *Microsoft Windows XP SP3* || *Apple Macintosh OS X 10.6.7* ||
| Internet Explorer 8.0 | Safari 5.0.5 |
| Firefox 4.0 | Firefox 4.0 |
| Flash 10.2.159.1 | Flash 10.2.159.1 |

Before you install/upgrade Flash Player, uninstall existing players          using the Adobe uninstall program.
There are uninstallers available for [Windows|http://kb2.adobe.com/cps/141/tn_14157.html] or [Macintosh|http://kb2.adobe.com/cps/865/cpsid_86551.html#ostype=m,prob1=uninst,os=m10.6,].

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h2. Microarray Data


h4. The Data Set

The website offers three types of searches to allow a user to:     (1) limit the visualization to a subset of probes (or genes) of interest [(Gene Search)|#Gene Search];     (2) use a 'seed' gene to find other genes with similar expression patterns [(Find Correlates)|#Correlative Search]; and     (3) compare expression between different anatomic regions [(Differential Search)|#Differential Search].



h3. Gene Search

To search for a gene category by disease, pathway, cell type or function, click on the relevant search term in the        tag cloud.        To search for probes associated with a specific gene or group of genes,        select the Gene Search radio button and type the gene name, gene symbol or Entrez Gene ID in the search box        (multiple genes searches require an OR between gene names) before clicking the Search button.
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h4. Boolean Syntax

The following special operators can be used to build queries:
|| Operator || Example Search Type || Example Query ||
| AND operator: & | Gene | [dopamine & receptor|http://human.brain-map.org/search.html?query=dopamine+%26+receptor&type=microarray] |
| OR operator: \| | Gene | [ABAT |ACHE|http://human.brain-map.org/search.html?query=ABAT+%7C+ACHE&type=microarray] |
| NOT operator: \! | Gene | ["dopamine receptor" \!DRD3|http://human.brain-map.org/search.html?query=%22dopamine+receptor%22+%21DRD3&type=microarray] |
* AND, OR and NOT may be used in place of their corresponding operators. They must be upper case.
* The AND operator (&) is implicit, so spaces between words  that are not separated by an operator will be treated like an &.
* OR (\|) has higher operator precedence than AND (&).
* Parenthesis can be used to group criteria, but nested parenthesis are not supported at this time.
* The NOT operator (\!)is not supported within parenthesis.

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h3. Correlative Search

In using gene expression databases, a "search by example" feature is also highly desirable 	  as genes with similar expression patterns may be related in function. The "Find Correlates" search       utility will accomplish this function. This search by example facility is also available 	  in the Allen Mouse Brain Atlas and Allen Developing Mouse Brain Atlas and the NIMH       Transcriptional Atlas of Human Brain Development.
To find other genes with profiles similar to your gene of interest, first select your probe by       clicking on any cell in the heat map related to that probe. You will see that probe listed in the       box above the right hand side of the heat map. Then select the brain structure(s) in which you       would like to see a similar expression pattern, and click "Find Correlates". This action will return       probes with a similar expression profile to brain region(s) in which you are interested. Only       regions selected for the search will be displayed. To see the search results across the entire brain,       turn off the "Restrict Domains" function at the bottom of the heat map.
You can see "anti-correlated" returns by toggling the sort order on column "r" or scrolling       to the bottom of the heatmap.

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h3. Differential Search

Another common usage of gene expression databases is to find genes that show enrichment of       expression in one region compared to another region. This type of query is supported by the       "Differential Search" mode. Select the "Differential Search" radio button. To find genes or       probes with a higher expression in one structure when compared to another structure, enter the       target brain structure in the top search box and your contrast region in the bottom search box and       click on the Search button.
Your search will return results in the two brain regions selected. The results will show higher       expression in the target region compared to the contrast region. (To view the expression patterns       of the returned probes over the entire brain, turn off the "Restrict Domains" function below the       heat map.) Search results are sorted either by p-value or fold change, indicated by the arrow on       the buttons over the column of genes. To alter the sort parameter, click on either the "p value" or       the "fold-change" buttons.
To perform the previous search in reverse, click the toggle button beside the Search button.

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h3. Data Visualization

Based on your search, the resulting microarray data sets are presented as a matrix with brain         structure (by individual donor) on the horizontal x-axis and gene probes on the vertical y-axis. The microarray data         is presented in a "heat map" format where the colors of the heat map correspond either to raw         data or to a normalized (z-score) expression level of a probe. Brain structures are organized such         that moving left to right on the x-axis is analogous to moving from anterior to posterior first in         the cortical areas, followed by subcortical areas, cerebellum and brainstem.

h4. Data Aggregation and Normalization

Unless viewing data from a single sample, the heat maps presented on this site are based on data aggregated within       brain structures ("Averaged Samples", see below). That is, when there are multiple samples for a given       structure, the value represented in the heat map will be the average of those sample values.

We further aggregate the expression values up the ontology tree, i.e. Frontal Lobe, 	  will have a single averaged expression value, which is the average value 	  for all samples belonging to the Frontal Lobe.

Data represented in the heat maps has been normalized across the entire data set 	  before it is aggregated, and is normalized again for each probe when the heat map is constructed.

h3. Heat Maps

The "heat map" is a visualization of the microarray values for the returned probes of interest. 	  Each row of the heat map represents a probe. 	  Each column of the heat map either represents a tissue sample or anatomical brain structure 	  depending on the selected Resolution (Coarse, Averaged Samples, or Sample). 	  The colors of the heat map are normalized expression values. 	  Default heat map colors are in the green -- red scale where the color green 	  should be interpreted as relatively low expression and red as relatively high expression within the scope of each       probe.

The color map used for the heat map display can be changed to suit the user. You can use the       color map bar at the bottom of the heat map to display different normalized (z-score) color representations       of the heat map data (i.e. blue-red vs. green-red)or you can visualize log2 normalized expression map where the color       scale ranges from dark blue, representing low expression, and passes through cyan, yellow, orange and finally to dark       red, representing high expression.

Clicking on a cell of the heat map will bring up detailed information in the area above the heat       map. In the panel on the left, information about the sampled anatomical structure is displayed.       The stack of structures represents the hierarchy from the structure ontology. For more details on       the ontology see [Ontology and Nomenclature|http://human.brain-map.org/content/Ontology.pdf], or       the Help section on the ontology viewer [here|#Ontology Browser].

Additional information is shown in the middle panel, and includes gene symbol, gene name, probe name,        the "log2" expression value and z-score and links to related data in other Allen Institute projects.        Links to donor meta-data are also included in this panel. Blue text indicates a hyperlink,        where there is more information available by clicking on the text.
The "Brain Explorer" link, when selected for the first time, will take you to a page where you         can download Brain Explorer® 2. Once Brain Explorer 2 is loaded, clicking on the [Brain Explorer|#Brain Explorer 2 Application] link will launch a desktop software application for viewing         the Atlas gene expression data in three dimensions.

The "Planar View" link launches the [multiplanar viewer|#Multiplanar Viewer] that shows the expression         profile for the selected probe in the context of the donor brain.

The columns of the heat map have a different meaning depending on the selected Resolution.         There are three options available from the drop-down menu under the heat map: Coarse,         Averaged Samples and Samples. If "Samples" is selected there is a one-to-one correspondence         between a column and a physical tissue sample. In the Atlas, there are         typically multiple samples for each structure of interest. This oversampling may provide         information on variability and spatial gradients. In "Averaged Samples" mode, all samples         belonging to the same designated structure are combined and averaged together. In "Coarse"         mode, the brain is divided into approximately 20 large neuroanatomic divisions or regions (e.g.         frontal lobe, occipital lobe, striatum, dorsal thalamus, ventral thalamus, etc.). Samples within         each partition are averaged together to provide a summary value for the partition.

Data from multiple brains may be viewed in two ways. By default, columns are grouped first by         donors then by structures, allowing a user to compare the expression profile of the individual         brains side-by-side. Grouping the columns initially by structures then by donors allows a user to         mix the data of the brains in the dataset within a combined brain structure profile. You can toggle         between the two groupings by clicking the toggle button over the scroll bar.

h4. Comparing Genes of Interest

You can add probes of interest to a collection for later viewing. 	  Check the checkbox at the left end of a search result row to add it to your collection. 	  Your choices are stored in a browser 'cookie' on your computer and will remain in effect 	  until you click the 'Clear Selections' button, or clear your web browser's cookie cache.

Click the 'View Selections' button to see all of your selections.

Please note that this feature requires that you have cookies enabled in your browser, 	  which is already the case for the great majority of users.[#Return to top]











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h3. Gene Detail

Clicking on the Gene Name or Gene Symbol of your Search results will take you to the Microarray Gene Detail page.

The Microarray Gene Detail page displays information about the gene including  	  Organism, Chromosome, Entrez Gene ID, related data from other Allen Brain Atlas resources,  	  Gene Name and Alternate Symbols.  	  Detailed expression heat maps for each probe are stacked by donor for a direct comparison between brains.  	  There is also a section of links to External Resources.

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h3. Probe Detail

Clicking on the Probe Name will take you to the Microarray Probe Detail page.

The Microarray Probe Detail page displays information about the probe including  	  Probe ID, Gene Symbol, Gene Name, Probe Name, NCBI Accession and GI numbers.  	  It also includes the probe type, length, GC percent and sequence information.  	  Detailed expression heat maps from each donor brain are stacked so as to directly compare the probe between brains. 	  There is also a section of links to External Resources.

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h3. Brain Explorer 2 Application

Brain Explorer 2 is a desktop software application for viewing human neuroanatomy and the       Allen Human Brain Atlas microarray gene expression data in the framework of the Magnetic       Resonance Images of the sampled brains.

Once you have chosen a gene of interest (by clicking on the heat map), you can explore a three       dimensional representation of its gene expression by clicking on the "Brain Explorer" link over       the heat map. When Brain Explorer opens, you will be taken to a screen that displays the Image       Viewer, the Structure Ontology Viewer, and the Gene List.

h4. Image Viewer

The Image Viewer will automatically show the 3D expression representations of your gene of interest on every       sampled brain. Cortical gene expression is overlaid on an inflated white       matter surface for each donor brain, with spots under the white surface representing gene       expression in the subcortical regions of the brain. A striped expression pattern on the cortical       surface is a result of having sampled from every other slab of cortical tissue. Under each       representative brain is the heat map for the probe you selected. Clicking on that heat map will       pinpoint the area in the brain from which the sample was taken.

The gene expression colors correspond to the settings in the Atlas with which you were viewing       the original heat map. To change the gene expression representation, click on the "Gene" tab in       the top left hand corner of your screen and choose either z-score or raw data representations of       the gene expression data.

A compass in the right hand corner of the image viewer depicted by a stylized head can be used       to rotate the brains by clicking and dragging your cursor. You can look at a single brain by       clicking on the magnifying glass above that brain. Choosing a data point, either by clicking on       the heat map below the brain or on a brain region itself, will bring up the gene symbol, the       location of the sample and the expression level and z-score in the left hand corner of the Image       Viewer.

You can zoom using either the wheel on your mouse or using the Zoom scrollbar in the lower       right hand corner of the Image Viewer.

h4. Structure Ontology Viewer

The Structure Ontology Viewer shows the entire collapsible ontology for the       human brain including the color coding used by our expert annotation team to visualize structural       boundaries. Two columns to the right of the ontology determine the type of data displayed in the       Image Viewer. "A" represents annotation and when checked, will show a visual representation of       that structure in the Image Viewer. "G" represents gene expression and when checked, will show       gene expression in that structural domain.

The default organization for the Structure Ontology is the Hierarchical View, but if you are       unfamiliar with the ontology, you can click on the Alphabetical View to see the structure list in       alphabetical order.

The Bookmarks tab is a space where you can create and save favorite views of the brain. Several       default views are already saved that will rotate the brain back into common viewing frames.

h4. Gene List

This section displays the gene probes you have selected and downloaded in this session. When       more than one gene probe has been downloaded, clicking on one probe will show its gene       expression profile in the image viewer. Right clicking on the gene probe name will bring up a       menu where you can view the gene detail page (Get Info), be taken to the Multiplanar View of       the probe (View Images) or copy the gene information for use in another application.

h4. Toolbar\\

| | Selects cursor rotation tool mode |
| | Selects cursor pan tool mode |
| | Selects cursor selection tool mode |
| | Toggle Sagittal Atlas section viewing |
| | Toggle Coronal Atlas section viewing |
| | Toggle Horizontal Atlas section viewing |
| | Centers the Viewer on the current pinpointed expression data point |
| | Turns on the cutting planes |
| | Toggles the Structure Ontology and Gene List View |

h4. Advanced Features

*Atlas Tab:*

You can show opaque three dimensional structures of the brain by "showing" or "hiding"       structures from this menu. The "Transparent" function allows you to see transparent views of       the structures to view the anatomical relationships between them.

Selecting the sagittal, coronal or horizontal sections (or clicking on one of the        section image buttons in the toolbar) will superimpose a single plane of the MRI images from each brain on your image       space. These planes can be moved once the selection tool mode button in the toolbar is selected. Selecting       "Show Annotation on Section" from this menu will color the MRI images according to the brain       structure ontology.

*Gene Tab:*

When you have a gene selected, the Gene Tab menu allows to you to show all expression, hide       all expression (for instance to then select a single structure) or toggle expression (for instance,       unselect your region of interest then toggle to see expression in only that region).

You can also show or remove threshold controls and choose the visual representation of your       data (raw data vs. z-score) from this menu.

To be taken to the gene detail page, select "Get Info". To see the Multiplanar view, choose       "View Images". These functions are also available by right-clicking on the gene name in the       Gene List.

*Clipping Planes:*

When this function is selected, either by toggling the        cutting tools button in the toolbar or selecting       "Clipping Planes" from the View drop down menu, you can make coronal, sagittal or horizontal       cuts in your view of the brain and related data. To cut in a particular plane, make sure the cursor       is in selection tool mode, and then click and drag on the plane you are interested in clipping.

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h3. Multiplanar Viewer

The Multiplanar Viewer shows sampling sites for microarray data 	  and indicates gene expression levels for a single probe 	  in coronal, sagittal and horizontal sections of MRI space for a given specimen. 	  Additional viewing frames show spatially correspondent histological data 	  at the slab and block level with anatomic annotations 	  and specific delineations of sampling sites for microarray data generation.

h4. Multiplanar Navigation

In the image to right you see the Multiplanar navigation controls. 	  Points from which microarray tissues samples were taken are colored 	  to show expression level, according to the active color map.

Click or click-and-drag to move the crosshairs on any of the three MRI views ports.

The various control and feedback components are labeled here 1 - 7:
# *Donor*: Identifier of the donor currently displayed in the viewer.
# *Probe Name*:  The label for the probe currently displayed in the viewer.
# *Permalink*: Click the permalink component to generate a URL 	      that will bring you back to this page with the current location settings.
# *Contrast*: Click and drag to move the contrast control.
# *Brain Structure*:  This field is updated to indicate the structure under         the crosshairs.  Click on the structure label to launch the ontology browser in a new window.
# *Expression Level*: This component reports both the raw expression value         and its z-score-normalized value.
# *Color Map Window & Level*: adjust the upper & lower bounds, or slide the entire control         to modify the range of colors used to map expression levels.

h4. Image and Probe Navigation

In the image at left you see the 2D images associated with the point selected     by the MRI crosshairs.  The viewer     on the left hand shows a larger view of the brain specimen, with a blue highlight     around the chunk of that specimen from which the current sample was taken.  The     viewer on the right hand shows a detailed view of that chunk, with structure annotations visible.

You can navigate from the image viewers as well. The strip of thumbnail images     at the bottom of each viewer shows all of the images from its parent specimen, in sectioning order.     Clicking on a thumbnail image in the left hand viewer will move the MRI crosshairs     and open a new set of images in the right hand viewer.  Click on one of the structures to move     the MRI crosshairs to the location where that structure was sampled.       As you move your mouse over the structures in the right hand viewer its name       will appear in the upper-left corner of the viewer.

Use the toolbar icons to add or remove structure annotations such as 	  structure outline,       structure colors,       and structure labels.       To show all specimen images from this block in order, including the Nissl, ISH, SMI-32 and pre\- 	  and post-cut LCM images, click . 	  To see the block face images, click . 	  Use the full-page viewer icon to launch a new full-page viewer in a new window for the current image set.

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h3. Microarray Specimen Magnetic Resonance Images (MRI)

Select the MRI tab to view the Microarray Specimen MRI page, or click on 		a Donor link in the Gene Detail or Probe Detail pages.

The Microarray Specimen MRI page displays axial, coronal and sagittal 		planar MRI images of the brain.  Drag the red axes in order to change the view coordinates. 		Donor information including Organism, Age, Sex, Ethnicity, and Postmortem Interval (PMI).

The MRI data files are available for download in NIFTI format by clicking on the T1, T2 and DTI links.

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h3. Raw Microarray Data Download

To download the raw microarray data for tissue samples in the Allen Human Brain Atlas, click on the Download tab.

h4. Searching by Structure

With the Search by Structure Name radio button selected, type in the text box to see some search suggestions 	  from the Allen Human Brain Atlas brain structure ontology. 	  Check the Include Descendents check box to include structures below the selected structure in the structure ontology.         Select from the list of suggestions, or just click the Search button to search for your structures.       For more details on the ontology see [Ontology and Nomenclature|http://human.brain-map.org/content/Ontology.pdf?1307563360],       also the Help section on the [Ontology Browser|#Ontology Browser].

For each tissue sample, the Microarray Data Download page has an  entry listing the Tissue Sample ID, the Structure name, 	  the RNA Integrity Number, the Experiment number, the Array number,  the sample Type, the RNA in Labeling Reaction, 	  the RNA in Array and a link to the raw microarray data file for the  tissue sample in Agilent Feature Extraction output file format.

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h3. Ontology Browser

Click on a Structure acronym link in the Microarray Search page or the Microarray Multiplanar View 	to open a new window with the Ontology Browser for the Allen Human Brain Atlas.

The expandable tree view of the anatomical structures is color coded and serves as a 	legend to the anatomic structures on other pages in the Allen Human Brain Atlas.

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h2. In Situ Hybridization (ISH) Data

Gene expression data is available as colorimetric _in situ_ hybridization (ISH) for specific brain regions. Images are grouped into [image series|#Image Series Information] that comprise an experiment. Experiments consist of slides from the same [specimen|#Specimen Detail Information] that receive the same treatment, whether it is Nissl staining or ISH with a probe for a particular [gene|#Gene Detail Information].

The projects include 1,000 Gene Survey in Cortex (Cortex Study), Schizophrenia Study, and Subcortex study. Please refer to the [In Situ Hybridization |http://human.brain-map.org/content/ISHOverview.pdf?1307563360] white paper in the ALLEN Human Brain Atlas Documentation tab for       the details.

Choose among the following options for retrieving the data:
* Search by Gene Category (from the tag cloud)
* Gene Search
* Search by Study

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h3. ISH Gene Search


h4. Gene Search

You can search for experiments associated with a gene using its  gene symbol, name, Homologene Group ID, or Entrez Gene ID. First, select       the "Gene" radio button, type the search term in the input box and  click the "Search" button. You will be offered       suggestions to choose from while you type, but you can also search  by typing the first three or more letters in its name or symbol and  appending       an asterisk ( * ) as a wildcard.

h4. Search by Study

Data includes ISH experiments from three separate projects  including: 1,000 Gene Survey in Cortex (Cortex Study), Schizophrenia  Study, and       Subcortex study. Please refer to the [In Situ Hybridization |http://human.brain-map.org/content/ISHOverview.pdf?1307563360] white paper in the ALLEN Human Brain Atlas and the [gene list|http://human.brain-map.org/content/HBA_ISHGeneList_2011-06_tgi.pdf] for details.

You can restrict your search to a single study and search for experiments associated with a gene from that study.

First, select the relevant radio button: Subcortex Study, Cortex  Study or Schizophrenia Study. You will then have a choice to limit your  search       based on additional criteria such as sex of the donor, hemisphere,  etc., depending on the study. Then type the search term in the input  box and       click the "Search" button. To see a list of genes surveyed in that  study, please look at the [gene list|http://human.brain-map.org/content/HBA_ISHGeneList_2011-06_tgi.pdf] in the documentation       tab. Clicking the "Search" button without any entry in the input  box will return a list of genes and the accompanying data for that  study.

The following search criteria can be specified in the text box to  the right of the categories. If you copy + paste in a list of terms  delimited       by tabs or carriage returns they will automatically be converted  into a list of search criteria separated by the OR operator ( \| ).
| * Gene symbol
* Gene name
* Entrez gene ID
* Homologene Group ID | * Allen Institute image series ID
* NCBI accession number
* Probe name |

h4. Boolean Syntax

The following special operators can be used to build queries:
|| Operator || Example Search Type || Example Query ||
| AND operator: & | Gene | [dopamine & receptor|http://human.brain-map.org/ish/human/imageseries/search/1.html?query=dopamine+%26+receptor] |
| OR operator: \| | Advanced | [ABAT |ACHE|http://human.brain-map.org/ish/human/imageseries/search/1.html?criteria=3%2C3%2C7%2C7%2C7%2C15%2C15%2C15%2C15%2C31&query=ABAT+%7C+ACHE&type=advanced] |
| NOT operator: \! | Gene | ["dopamine receptor" \!DRD3|http://human.brain-map.org/ish/human/imageseries/search/1.html?query=%22dopamine+receptor%22+%21DRD3] |
* AND, OR and NOT may be used in place of their corresponding operators. They must be upper case.
* The AND operator (&) is implicit, so spaces between words  that are not separated by an operator will be treated like an &.
* OR (\|) has higher operator precedence than AND (&).
* Parenthesis can be used to group criteria, but nested parenthesis are not supported at this time.
* The NOT operator (\!)is not supported within parenthesis.

h3. Search Results

Click a column heading to sort the search results. Click it again  to toggle ascending to descending order. ISH search results include the       following columns:
|| Column || Description ||
| Select | Add the image series to your selections by clicking a checkbox. The selected series can be opened in the [Zoom and Pan Image Viewer|#Viewing Images] by clicking, "View Selected Experiments." |
| Gene Symbol | Click the gene symbol to view the experiments associated with it |
| Gene Name | Full gene name |
| Condition | Control or Disease State |
| Tissue Location | Specimen origin |
| Age | Donor age |
| Sex | Male/Female |
| Specimen | Click the Allen Institute specimen ID to view its [details|#Specimen Detail Information] |
| Image Series | Click the Allen Institute image series ID to view the experiment's details |
| Donor | Allen Institute donor ID |
| Related Data | Click the "Related Data" button to display a list of Allen  Brain Atlas       resources for the species indicated. Please note that  the current project is excluded       from the list of suggestions. For  example, if a "human" link is displayed while viewing       human  microarray data, it refers to related ISH data. |
Select an image series by clicking the checkbox in the first column,  then click the "View Selected Experiments" button to view all of     your selections' images. Click "Clear Selection" to deselect all of  your selections, or click "View Cart" to manage them.

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h3. Viewing Images

h4. Zoom and Pan (ZAP) Image Viewer

The ZAP Image Viewer allows you to navigate through  an image series' thumbnails to select an image to view at higher  resolution.     Once selected, you can manipulate it with your mouse and use the [keyboard|#Keyboard Commands] or [toolbar|#Toolbar] to     take additional actions.

Choose a different viewer size by selecting it from the dropdown  menu above the viewer(s). If you are viewing more than one image series,  choose a     different table layout by selecting a different number of columns.  Drag viewers to other cells in the table to rearrange them.

Multiple image series can be opened on the same Web page to enable  side-by-side comparisons. You can swap viewers' locations on the page by     clicking on the first viewer's title bar and dragging it to the  second viewer's location.

The gene symbol or treatment type is displayed in the title bar  along with the Allen Institute image series ID. Additional details are  displayed     across the top of the viewing area, including the image index,  tissue index, and tissue location.

Thumbnails for the entire image series are displayed across the  bottom of the viewer in section order. Click a thumbnail to select it  for     viewing, or use the [keyboard|#Keyboard Commands] to navigate through the set. The current selection is outlined in black.

h4. Side by Side Nissl Viewing

Once you click on the full screen viewer button, you will be taken to a screen with side by side viewers. The left       hand viewer shows the ISH image series and the right hand viewer displays the Nissl image series from the same       specimen block. To show the nearest Nissl section to the ISH image you are interested in, click the "Sync" checkbox.       Clicking on another ISH image will automatically display its nearest Nissl section. Clicking on an image thumbnail in       the Nissl image series will automatically take you to the nearest ISH image. While the "Sync" box is checked       the Pan and Zoom functions will affect both ISH and Nissl images.

h4. Scale Bar

Shows the current viewing resolution of the image, in microns.  This value dynamically changes as you zoom in/out of the image. You can  position       the scale bar anywhere on the main image by dragging the scale bar  by its ruler.

You can toggle the orientation of the scale bar from horizontal to vertical by clicking on the scale bar text.


h4. Toolbar

| | Show current image in a full-screen viewer, on its own page |
| | Open a new window to view the image series' details |
| | Select ISH, Nissl, or [Expression|#Expression Mask Colors] image type |
| | Move the slider bar to the left to intensify the contrast or color |

h4. Keyboard Commands

| F | Advance to the next image in the series |
| D | Go back to the previous image |
| R | Advance to the last image in the series |
| E | Go back to the first image in the series |
| A | Zoom in |
| Z | Zoom out |
| + | Zoom in (may need to press shift key) |
| \- | Zoom out |

h4. Expression Mask Colors

The Expression Mask image display highlights those cells that have  the highest probability of gene expression using a heat map color scale  (from       low/blue to high/red).

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h3. Specimen Detail Information


h4. Specimen Block Layout

Specimens are received as variable sized blocks of frozen tissue. Before they are       sectioned for ISH experiments they are divided into a number of sub-specimens.       Throughout this site, when we refer to a specimen we are actually referring to one       of these sub-specimens.

The specimen block layout diagram is intended to put the current sub-specimen       in context of its original tissue block, and to help navigate to nearby sub-specimens.

In the block diagram, the green block       represents the current sub-specimen. Sibling sub-specimens are shown as grey blocks.       Clicking on one of the siblings updates the current page to show the sibling's information.

h4. Donor/Specimen Metadata

 *pH* \- tissue sample pH
*RNA Integrity Number* \- metric indicating RNA integrity from tissue. Ranges from 1 to 10 (degraded to intact RNA)
*Postmortem Interval* \- hours between time of death and time tissue samples frozen
*Hemisphere* \- right or left hemisphere tissue origination
*Tissue Location* \- tissue origination in brain
*Specimen ID* \- internal ID
*Sex* \- male or female
*Race* \- ethnicity
*Age* \- years
*Handedness* \- right, left, or ambidextrous
*Disease Categories* \- control or schizophrenia
*Smoker* \- yes or no
*Donor ID* \- internal ID

h4. Sectioning Diagram

The sectioning diagram attempts to depict the relationship between the sections       taken from a specimen, the position of each section, and the genes for which       experiments have been run on those sections.

Each section consists of 100% of the specimen in the plane of sectioning.       The section number, or "section index" is an indicator of relative       depth into the specimen.

To the left of the section diagram is a preview image. As you move your mouse pointer       over the section diagram squares, the preview will be updated to show the corresponding image.       You can get a larger view of the preview image by clicking your mouse on the section squares       to launch an image viewer on a separate page.

Each of the colored squares at the top of the diagram represents one section. By default,       the sections are ordered by section index. The different colors are mapped to the       different genes tested against each section. The color-to-gene mappings can be found       in the rectangular gene symbol map appearing below the set of sections.

Each rectangle in       the gene symbol map has the same color as one or more of the section squares, and represents       either the genes targeted for ISH, or the particular stain applied to the corresponding section blocks.

Hovering the mouse pointer over the rectangles will highlight the associated       section squares for easy identification.       Each rectangle is labeled with either a gene symbol       or a stain treatment abbreviation.

You can click your mouse on the rectangles to go to an Image Summary page, where you can get       more information about the section images generated from a particular treatment, and get summary information about       gene probes.

h4. Diagram tools

On the right of the titlebar of the Sectioning Diagram, you will find two diagram display tools, which are       described below.

h4. Contrast Slider

Drag this slider to the left or right to adjust the contrast of the preview image. Dragging the slider to the       left makes the image lighter, dragging the slider to the right makes the image darker.

h4. Section Ordering

Click this button to sort the section diagram by gene rather than section index. Click it again         to return to the default ordering.

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h3. Gene Detail Information

This page summarizes the data regarding the selected gene. The main  section details its full name, entrez gene id, alternate     gene symbols, chromosome, organism, links to related data in other  projects, and gene categories that have been applied to it.     A link below this section allows you to bring up a summary of all of  the experiments (image series) for this gene.

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h3. Image Series Information

The image series details include the gene and probe associated with the experiment, as well as information regarding the [specimen|#Specimen Detail Information].

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