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.
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.
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.
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.
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
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.
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.
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.
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.
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.
To download the raw microarray data for tissue samples in the Allen Human Brain Atlas, click on the Download tab.
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
and Nomenclature, also the Help section on the Ontology
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.
Gene expression data is available as colorimetric in situ hybridization (ISH) for specific brain regions. Images are grouped into image series that comprise an experiment. Experiments consist of slides from the same specimen that receive the same treatment, whether it is Nissl staining or ISH with a probe for a particular gene.
The projects include 1,000 Gene Survey in Cortex (Cortex Study), Schizophrenia Study, and Subcortex study. Please refer to the In Situ Hybridization white paper in the ALLEN Human Brain Atlas Documentation tab for the details.
Choose among the following options for retrieving the data:
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.
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 white paper in the ALLEN Human Brain Atlas and the gene list 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 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 ( | ).
Entrez gene ID
Homologene Group ID
Allen Institute image series ID
NCBI accession number
The following special operators can be used to build queries:
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.
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:
Add the image series to your selections by clicking a checkbox. The selected series can be opened in the Zoom and Pan Image Viewer by clicking, "View Selected Experiments."
Click the gene symbol to view the experiments associated with it
Full gene name
Control or Disease State
Click the Allen Institute specimen ID to view its details
Click the Allen Institute image series ID to view the experiment's details
Allen Institute donor ID
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.
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 or 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 to navigate through the set. The current selection is outlined in black.
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.
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.
Show current image in a full-screen viewer, on its own page
Open a new window to view the image series' details
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.
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
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.
On the right of the titlebar of the Sectioning Diagram, you will find two diagram display tools, which are described below.
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.
Click this button to sort the section diagram by gene rather than section index. Click it again to return to the default ordering.
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.