In situ hybridization (ISH) data for NHP Atlas


This study collected high-resolution in situ hybridization image data covering selected genes during development. For a list of genes, please see the gene list under the Documentation tab in the main banner of the web application. The data includes a survey of five major brain regions during four postnatal developmental periods for genes clinically important in a variety of human neurodevelopmental disorders, serial analysis of selected genes across the entire adult brain, focusing on cellular marker genes, genes with cortical area specificity and gene families important to neural function and whole brain serial analysis of genes ENC1 and GAP43 to aid neuroanatomical delineations for prenatal microdissection microarray.

You can search this data using Gene Search by typing a gene-related term into a search field, searching by Gene Classification, using the Advanced Gene Search feature or with the Annotation Search which utilizes manual annotation of the image data.

Gene Search

To search for a gene, select the Gene Search radio button and then type the gene symbol, gene name, gene aliases/alternate symbols, predicted human homolog gene symbol, NCBI Accession Number, or Entrez Gene Id into the search box. A list of suggested options will open, and you can select from one of those suggestions.

Gene Classification

The ISH data only includes a select number of genes so you can browse the data using the Gene Classification menus. When you land on the ISH Data page, the categories are displayed allowing you to search the genes included for each category.

If you are on any other page in the ISH project, click on the “Gene Classification” radio button and select a category from the drop-down menu.


Advanced Gene Search

The Advanced Search allows you to narrow your gene search by gender, developmental stage and by tissue location. When you select the “Advanced Gene Search” radio button, you will be able to deselect the categories that don’t pertain to your search. If you do not enter a gene in the search box, all genes that fulfill your search criteria will be returned.

Annotation Search

Experiments conducted on the post-natal stages were manually annotated for their Expression Intensity and their Expression Density.

For a detailed description of the manual annotation process, please see the ISH whitepaper in the NHP Documentation. Briefly, both the expression intensity and the expression density were scored on a scale from 1-5.

To perform an annotation search, first choose the brain region or structure of interest from the ontology. Clicking in the Structure search box will open the drop-down menu with all the available structures or regions. Either begin typing your structure into the search box or browse the list in the drop-down. Once you have chosen a structure, choose the developmental stage, the expression intensity and density you are interested in seeing and then click “Search”.

If you would like to include more than one structure in your search, click the “+” button, and repeat the above instructions. If two or more structures (or ages or intensities or densities) are selected in a single row, the search will find all results that match any one of the criteria (i.e. an “OR” search within a row). If more than one row is used, only genes that meet the criteria in ALL rows of the search will be returned (i.e. an “AND” search between rows).

Search Results

Searches will return a list of experiments based on the input search criteria. Each row includes the following information.

Column Description
image Add the experiment to your selections by clicking the checkbox
Experimental ID Clicking on this link will open the Experimental Details page
Gene Symbol (Homolog) Clicking the Gene Symbol will return Experimental Details pages for all experiments with this gene
Gene Name Full gene name
Tissue Location Tissue location of the sample
Age Ages based on search criteria
Specimen ID Clicking this link will open the Specimen Detail page
Donor ID Allen Institute Donor ID
Related Data Links to other projects conducted with this particular gene


You can sort your results by any any of the columns in either ascending or descending order (by checking the box next to your sort parameter).

Select the experiments to view in greater detail by clicking on the checkboxes next to your experiments of interest. Experiments will be saved in your cache until you select the “Clear Selections” button at the bottom of the page. After selecting one or more experiments, click the “View Selections” button.

At the bottom of the search results table, there is a link to an XML document containing all of the data in the result set.

Viewing Images

Clicking on the “View Selections” button will open all selected experiments in a new window within individual viewers. The individual experiments can be moved around by clicking and dragging on the title bar and number of columns in this window can be changed by clicking on the gear in the top right-hand corner of the screen.

Zoom and Pan (ZAP) Image Viewer

The ZAP image viewer allows you to navigate through an experiment’s images by selecting from one of the thumbnail images along the bottom to select an image to view at higher resolution. The current selection is outlined in black. Once selected, you can Zoom and Pan using the onscreen navigation buttons or use the keyboard commands or the toolbar icons to take additional actions.

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

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.

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


Icon Description
image Adjust contrast on the main image
image Select ISH, Nissl, or Expression image type
image View image series in contact sheet form
image Show current image in a High resolution Image Viewer, on its own page
image Open a new window to view the Experimental Details Page
image Close the current image viewer

High Resolution Image Viewer

The high resolution image viewer is a viewer that opens in a new window and allows you to get a more detailed view of the experimental images in a structural and cytoarchitectural context.

Side-by-Side Nissl Viewing

Opening the High Resolution Image Viewer will open a new window with your ISH experiment and a side-by-side view of the nearest Nissl image. The left hand viewer shows the ISH image series and the right hand viewer displays the Nissl image series from the same specimen block. By default, the nearest Nissl section to the ISH image you are interested in will be shown and synched with the section you are viewing. Click the “Sync” checkbox to manually correct any synching between the images. 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.

Colored circles in the Nissl slides are hotspots - regions that when moused over list the brain regions manually labeled by our Annotation team.

To download an image, click on the image button.

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).


Experimental Details

Clicking on the Experiment ID from the search results page or the “i” icon from the image viewers will take you to a page which includes metadata on the experiment, the specimen and the probe as well as related institute data links and a ZAP viewer for all images in the series.


This box gives you information on the gene assayed, the probe type and orientation, the plane of section and the kind of treatment (i.e. ISH, Nissl)


This box lists the Donor ID in the title bar and lists the Specimen (Clicking this link will open the Specimen Detail information), organism, age, sex, tissue location and hemisphere.


This box lists the Probe ID in the title bar and includes the type of probe, orientation, NCBI Accession #, GI # and the sequences of the forward and reverse primers so you can recreate this probe for your experiments. It also includes the probe sequence for your reference.

Specimen Detail

Clicking on the specimen link from the search results page or on the specimen link in the experiment details page will take you to detailed specimen information. Specimen detail information includes Specimen Information, Section Information, Gene Information and an Image Viewer.

Donor/Specimen Metadata

Specimen ID - internal ID
Age - years
Sex - male or female
Tissue Location - tissue origination in brain
Hemisphere - right or left hemisphere tissue origination

Section Information

The section information box lists information from the current gene pictured in the image viewer including the gene name, the Experiment ID, the section number, the treatment and which study the data came from.

Gene Information

The Gene information section lists the genes that were assayed in this specimen block.


By default, all genes from this specimen are selected for viewing. You can select fewer genes/histological stains to view in the image viewer by first clicking the “Gene” checkbox, then selecting the checkboxes next to the gene/stain(s) you would like to view.

Image Viewer

The viewer displays the image from the current gene listed in the section information box. Below the image, there is an indicator of the position in the specimen block of that particular section, as well as a visualization of the depth of the section into the block. You can view the sections in order (default or by clicking the image button) or grouped by gene (image button).

When you click on the magnifying glass in the bottom of the image viewer, a new window will open with a magnified view the area in the image viewer outlined by the red box. you can increase or decrease the magnification by clicking the “+” or the “-” buttons.

This data can be downloaded as an XML file.