Searching
There are two general ways to search for image data, either by typing a gene-related term into a search field, or by
selecting predefined conditions of gene, structure, and age by clicking on check boxes. The latter search method is
further subdivided into two categories, a Structure Search and an Age Search. There is also a more specific search
modality the lets you search on regions of interest within a larger anatomic structure; see
Anatomic Search for details about this type of search. Regardless of search type, the
search results are similar for all methods, resulting in one or more tables with multiple rows, each row representing
summary data about ISH image sections and their related images in the sectioning series.
See
Search Results for details about the summary tables.
Gene Search
The gene search uses a gene symbol- and gene name-based incremental search field. As you type in characters, a
drop down list appears below the search field showing potential matches against gene symbol, gene name, gene
aliases/alternate symbols, predicted human homolog gene symbol, NCBI Accession Number, or Entrez Gene Id.
You can use your arrow keys or the mouse to highlight the desired entry.
If you're using your mouse, click on the desired entry to select it, then press your
Return or Enter key or click the Go button to the right of the field to perform the search.
If you're using arrow keys, just press Return or Enter and the search will be run.
If you just want to search on what you've typed in the search field, click on the Go button to the right of the field.
This will base the search on what you've typed, ignoring anything in the drop down menu.
Return to Contents
Structure Search
Use the Structure Search when you want to filter your image search results primarily on brain structures, then by
specific ages and genes.
Each structure is named on a long, wide accordion button. Hidden beneath each accordion button
are other nested accordion buttons, which in turn contain check box options for specifying ages and genes.
Clicking on an accordion button shows/hides its nested contents.
For example, click on the Hippocampus accordion button to reveal nested Refine filter by Age and Refine
filter by Gene accordion buttons.
Click on Refine filter by Age accordion button, which reveals Age check boxes. The
Select all and
Clear all buttons make it easy to select/clear all the Age check boxes.
Click on the Refine filter by Gene accordion button to reveal Gene check boxes. In the image to the
right, the Refine filter by Age accordion is closed. Each checkbox is followed by a Macaque gene symbol.
The text is colored black if the gene was assayed selectively on the structure being queried, and blue if the
gene is part of a set of 13 pan genes that were analyzed across all brain structures and ages. You'll notice
that some gene symbols are followed by another gene symbol enclosed in parenthesis. This additional gene symbol
is the predicted human homolog, included in cases where the macaque sequence currently remains unannotated.
Pressing the Go button will conduct a Structure search for all Structures listed above the button which have options
selected for both Age and Gene. You need at least one selection from Age and one from Gene before a search will be
conducted for the particular Structure.
Return to Contents
Age Search
Use the Age Search when you want to filter your search results primarily on age, then by specific
structures and genes.
Each age is named on a long, wide accordion button. Hidden beneath each accordion button
are other nested accordion buttons, which in turn contain check box options for specifying structures and genes.
Clicking on an accordion button shows/hides its nested contents.
For example, click on the 0 months accordion button to reveal nested Refine filter by Structure
and Refine filter by Gene accordion buttons.
Click on Refine filter by Structure accordion button, which reveals Structure check boxes. The
Select all and
Clear all buttons make it easy to select/clear all the Structure check boxes.
Click on the Refine filter by Gene accordion button to reveal Gene check boxes. In the image to the
right, the Refine filter by Age accordion is closed. Each checkbox is followed by a Macaque gene symbol.
The text is colored black if the gene was assayed selectively on the structure being queried, and blue if the
gene is part of a set of 13 pan genes that were analyzed across all brain structures and ages. You'll notice
that some gene symbols are followed by another gene symbol enclosed in parenthesis. This additional gene symbol
is the predicted human homolog, included in cases where the macaque sequence currently remains unannotated.
Pressing the Go button will conduct an Age search for all Ages listed above the button which have options
selected for both Structure and Gene. You need at least one selection from Structure and one from Gene before a
search will be conducted for the particular Age.
Return to Contents
Anatomic Search
Use the Anatomic Search to perform spaciotemporal searches on particular anatomic substructures, finding images
that meet user-selectable values of gene expression or cell density. See the
Anatomic Search white paper
for details.
This search option is accessed clicking on the "Anatomic Search" menu bar item. On the search page are two tabbed
panels, each offering a different search modality.
The first tab is labelled "Two substructures, same age." This tab lets you pick two anatomic substructures that
meet selected magnitude criterion for either gene expression or cell density. The search is further constrained in
that both substructures must be from a donor of the same age; you can select an age of 0, 3, 12, or 24 months.
The second tab is labelled "Same substructure, two ages." This tab lets you pick a single anatomic substructure,
then specifying values for gene expression or cell density anticipated at two different ages.
Once all search criterion are selected, press the "Go" button at the botton of the tab panel to conduct a search.
Each of the two tab panels is described in detail below.
Two substructures, same age
Here is an overview image of the tab panel contents. It is structured as a form, where you choose:
1) Measurement type, either gene expression or cell density,
2) Anatomic region of interest by selecting a structure and substructure
3) Age
Each of these three form areas are discussed in detail below.
1) Select measurement type by clicking on one of the two radio buttons. Both types of measurement were scored
against the same tissue, but you can direct your search against one measurement or the other.
2a) In this section, you specify two different anatomic regions of interests, and specify the magnitude of the
type of measurement that you expect for each region. The region of interest is specified by selection an general
structure via a pull down menu. Once you've made this selection, an appropriate set of substructure choices is
presented in the form of a table or a tree. Click on a substructure choice to finish defining the region of
interest. Lastly, specify the magnitude of measurement by using the slider control. You can either select an
inclusive range of values or a discreet value by dragging the slider control handles to the right or left.
2b) This set of radio buttons determines the search logic applied to your two sets of structure-and-magnitude search
criterion. Normally, you want to find images that successfully match both sets of criterion; this is done by
using the radio button selection, "both Substructure 1 AND Substructure 2". Sometimes these matching rules are too
strict, and few or no results are returned. You might want to see the set of matches that meet either the first or
the second sets, all presented together. In that case, use the radio button selection, "either Substructure 1 OR
Substructure 2."
3) This pull down menu is used to specify the age constraint applied to the two structure-and-magnitude selections.
The ages are 0 mo, 3 mo, 12 mo, and 48 mo. There is an additional "express" option in the menu called "* All ages",
and when selected, causes four separate searches to be run, one at each age. The results from the four searches
are combined on the same search results page for easy comparison.
With all form selections completed, pressing the Go button performs the image search.
Search results are discussed in the Search Results sections of the this Help document.
Same substructure, two ages
Here is an overview image of the tab panel contents. It is structured as a form, where you choose:
1) Measurement type, either gene expression or cell density,
2) Anatomic region of interest by selecting a structure and substructure
3) Age
Each of these three form areas are discussed in detail below.
1) Select measurement type by clicking on one of the two radio buttons. Both types of measurement were scored
against the same tissue, but you can direct your search against one measurement or the other.
2) In this section, you specify an anatomic regions of interests by first selecting a general structure via a pull
down menu. Once you've made this selection, an appropriate set of substructure choices is presented in the form of
a table or a tree. Click on a substructure choice to finish defining the region of interest.
3a) Specify the two time points of interest for the substructure chosen in the previous section, and select the
magnitude of the gene expression or cell density anticipated at each age. Use the pull down menus to select one
of the four time points, either 0, 3, 12, or 48 months. Use the slider controls to select magnitude, selecting
either an inclusive range of values or a discreet value by dragging the slider control handles to the right or left.
3b) This set of radio buttons determines the search logic applied to your two sets of age-and-magnitude search
criterion. Normally, you want to find images that successfully match both sets of criterion; this is done by
using the radio button selection, "both Age 1 AND Age 2". Sometimes these matching rules are too
strict, and few or no results are returned. You might want to see the set of matches that meet either the first or
the second sets, all presented together. In that case, use the radio button selection, "either Age 1 OR
Age 2."
With all form selections completed, pressing the Go button performs the image search.
Search results are discussed in the Search Results sections of the this Help document.
Return to Contents
Search Results
After conducting a Gene, Structure, Age or Anatomic search, the results of the search are presented on a Search Results page
in the form of one or more tables. Each row of data is a summary of information about a set of tissue
sections and their associated images. Each column provides information and/or a link to more detailed
information.
The first row contains the name of the columns. By default, the rows are sorted by the column whose name has a
small
triangle to the right of the name.
Sorting
You can sort the rows by column contents on any column whose name appears green.
Clicking on a green column name will sort it in ascending order; a second click will reverse the sort order.
Getting more detailed information
The Gene symbol, Specimen ID and Image series ID column items all link to more detailed information pages:
Viewing selected rows data
You can select multiple rows so that each row's images can be viewed and compared on a single page.
Click the check
box at the far left of the desired rows, then click the
View selected data button. Selection is not
limited
to the current page, you add rows found on other pages of the current search results. As a convenience, you can
use the check box in the column header to toggle all of the row check boxes on or off. This action only affects
the currently-viewed page's rows.
The button
Clear all selections will unselect all rows across all pages of the current search results
table.
To the right is an example of what you might see after selecting four rows and pressing the
View selected
data button. Each row's images are displayed in a thumbnail viewer, with summary information presented on
a side panel to the right of the viewer. You can reposition these viewer by dragging and dropping them into
a different appearance order. The viewer's title bar text is draggable; click down on the title and drag the
viewer on top of another viewer, the two viewers will swap positions. If you want to remove one or more
See the
Thumbnail Image Viewer section for more details about the viewer operations.
XML
As shown in the image above, at the bottom of the table there is a link to an XML document containing
all of the data in the result set.
Return to Contents
Image Series Details Page
This page summarizes data about the selected gene into three blocks, a general summary, a transcript and
riboprobe information section, and a display of thumbnails of all images in the series. You can click on any
thumbnail image to open the image in the Full Screen Image Viewer.
XML
The XML link at the bottom of the page will produce an XML document containing all page data.
Return to Contents
Specimen Details
This page provides information about the tissue at a sectioning perspective. There is a general information block,
"Donor/Specimen", followed by a detailed "Tissue section schema" block.
Tissue section schema
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. In this diagram, each section is
numbered with its "section index" which is relative depth into the specimen.
Each of the colored squares in 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. Clicking on a square will open the image corresponding to the section
in the Full Screen Image Viewer.
To the left of the section diagram is a preview image. As you move your mouse pointer
over the section diagram the preview will be updated to show the corresponding image.
Below the sections squares are colored rectangles which match the section square colors. These rectangles
represent the gene symbols map associated with each section. Clicking on a gene symbol rectangle takes you to
the Image Series Details page.
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.
At right is an example of the section diagram ordered by gene.
Return to Contents
Thumbnail Image Viewer
The thumbnail image viewer is used to get an overview of ISH, Nissl, and Expression mask images in an image series.
Overview
1 - Title bar. Shows Image Series ID, and a number of buttons
2 - Main image area
3 - Image selector, arranged in section order. Current image is outlined in black
4 - Information sidebar.
Buttons
Show ISH images
Show nearest Nissl images
Show Expression mask images
Show current image in a full-screen viewer, on it's own page
Close this thumbnail viewer
Image Manipulation
You can zoom in/out on the main image, pan to different areas of the image, and select different images in the series
for viewing.
Image zooming can be done by mouse or keyboard. Using the mouse, click on the main image. You can now use the
mouse wheel to zoom in/out on the image. Use keyboard keys A and Z (not shifted) to zoom in and out. On Macintosh
computers, the zoom keys may be - and +.
Image panning can be done by mouse or keyboard. Using the mouse, click on the main image and drag it to pan to a
new position. Using the keyboard, the cursor keys will allow panning in up, down, right and left directions.
Switching to different images in the series can be done by mouse or keyboard. When using the mouse, just click on
the appropriate image on the image selector area below the main image. When using the keyboard, these options are
available:
- F - next image
- D - previous image
- R - last image
- E - first image
Full Screen Image Viewer
The full screen image viewer is a larger version of the thumbnail image viewer,
allowing you to get a more detailed look at the images. It has most of the same features as the thumbnail image
viewer, and a few differences. Please refer to the
Thumbnail Image Viewer section
for a discussion of the features held in common between the two viewers.
Unique Features
1 - Buttons
2 - Scale Bar
Buttons
Recenter the image. Useful if you've panned
image and you need to restore a known starting location.
Click to hide the scale bar, click again
to show the scale bar.
Create a permalink to the current image that
you can bookmark or email. The permalink replaces the current URL shown on your web browser.
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
