h2. Gene Search

To search for a specific gene or group of genes, type its gene symbol, name, Homologene Group ID, or Entrez Gene ID into the search box. Make sure the Gene radio button is selected 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. You can also browse by gene category by clicking on a word in the tag cloud. The font size of the words in the cloud correspond to the number of genes linked to each category. Genes were linked to each category using online tools such as the PANTHER.


!ISH_Search.PNG|border=1!


You can sort the search results or further refine your query using the [#Advanced Search] feature.

h3. Advanced Search

Several additional search criteria can be used to build a query using "Advanced Search." The categories that can be selected for building a query include:

||Category ||	Values||
|Sex 	|male, female|
|Smoker 	|smoker, non-smoker|
|Hemisphere 	|left, right|
|Handedness 	|left, right|
|Age 	|birth to 19 years, 20+ years|
|Tissue Location 	|Amygdala, Hippocampus, Medial Prefrontal Cortex, Ventral Striatum, Visual Cortex|

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: \| | Gene | {menulink:custom|link=http://human.brain-map.org/search.html?query=ABAT+%7C+ACHE&type=microarray|target=_blank}ABAT\|ACHE{menulink} |
| 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.
* Enclose search terms in quotation marks to avoid confusion with boolean operators. For example, hyphenated words should be enclosed in quotation marks (i.e. "ATP-binding").

h4. Search Results

Search results can be sorted by up to four categories indicated by the drop down menus. Search categories are prioritized from left to right and include all searchable columns. The checkbox labeled "asc" indicates the sorting direction for each column. "asc" stands for ascending order, so when checked, the sort progresses from a to z , or 1 to n, depending on whether the column is alphabetic or numeric. Leaving the box unchecked sorts the column in descending order, that is z to a, or n to 1.


!ish_search_results.PNG|border=1!

||Column 	||Description||
|!checkbox_column.png|align=center! |Add the image series to your selections by clicking a checkbox. The selected series can be opened in the [Zoom and Pan Image Viewer|#ISH - Image Viewing] by clicking, "View Selected Experiments."|
|Gene Symbol 	|Click the gene symbol to view the experiments associated with it|
|Gene Name 	|Full gene name|
|Entrez Gene ID 	|Accession number|
|Tissue Location 	|Specimen origin|
|Age 	|Donor age|
|Sex 	|Male/Female|
|Specimen 	|Click the Allen Institute specimen ID to view its details|
|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. ISH - Image Viewing


!ish_zap.png|align=left,border=1, hspace=5, vspace=8! The Zoom and Pan (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 donor age, 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.

h4. Scale Bar


!help_vScaleBar.png!  !help_hScaleBar.png!

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

||Icon||Description||
|!showIshInSIV.png!|Show current image in a full-screen viewer with [#side by side Nissl] comparison|
|!IshInfo.png!|Open a new window to view the image series' details|
|!ish_zap_image_type.png!|Select ISH, Nissl, or Expression image type|
|!ish_zap_contrast.png!|Move the slider bar to the left to intensify the contrast or color|

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.  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.

!ish_side_by_side_nissl.png|border=1!

h4. Keyboard Commands

||*Key*||*Description*||
|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


!help_ishColorMap.png|border=1!

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).


h4. ISH - Specimen Details

To reach the Specimen Detail page, click on the image series detail icon, then click on the blue texted specimen ID link, or click directly on the specimen ID from the original search page.

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.

h4. Donor/Specimen Metadata

||Name||Description||
|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|
|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.

h5. 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 darker, dragging the slider to the right makes the image lighter.

h5. 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.



ISH - Gene Details

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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ISH - Image Series Details

The image series details include the gene and probe associated with the experiment, as well as information regarding the specimen.
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