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Several experiments can be selected to view side-by-side and/or in the context of our reference data by checking the boxes next to the experiments. Once you have selected the experiments you want to view, click the "View Selections" button. Those experiments will be available in your cart to view in the #Experiment Experiment Image Viewer until you clear your cache or click the "Clear Selections" button.

Once you have narrowed your search and want to delve deeper into an individual experiment, open the #Experiment Experiment Summary View by clicking on a circle in the 3-D search result visualization or an experiment in the list.

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This search has all the same functional capabilities as #Source Source Search with the added ability to filter your search by limiting the results to experiments where the projection signal passes through a given structure(s).

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Several experiments can be selected to view side-by-side and/or in the context of our reference data by checking the boxes next to the experiments. Once you have selected the experiments you want to view, click the "View Selections" button. Those experiments will be available in your cart to view in the #Experiment Experiment Image Viewer until you clear your cache or click the "Clear Selections" button.

Once you have narrowed your search and want to delve deeper into an individual experiment, open the #Experiment Experiment Summary View by clicking on a circle in the 3-D search result visualization or an experiment in the list.

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Several experiments can be selected to view side-by-side and/or in the context of our reference data by checking the boxes next to the experiments. Once you have selected the experiments you want to view, click the "View Selections" button. Those experiments will be available in your cart to view in the #Experiment Experiment Image Viewer until you clear your cache or click the "Clear Selections" button.

Once you have narrowed your search and want to delve deeper into an individual experiment, open the #Experiment Experiment Summary View by clicking on a circle in the 3-D search result visualization or an experiment in the list.

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Hovering your mouse over an experiment will highlight that injection site in the 3-D search result visualization. Rotating the image in either the horizontal or vertical planes gives better access to view the selected experiments. To take a closer look at a particular experiment, click on that experiment, either in the list or on the 3-D search result visualization. Once an experiment has been chosen in this manner, a new panel of images and options will load on the right labeled by the Experiment ID number and the injection site structure. This view includes a section images viewer, a projection density image viewer, a transgenic characterization box, an injection summary for the rAAV virus injection and the targeting CAV injection summary (when appropriate) and a correlative search box. Characterization of the transgenic lines used in this study has been carried out, and can be inspected from the link in the Transgenic Characterization box. If viewing an experiment from the Retinal Projectome, a whole mount view of the retina is available from a link in the Transgenic Line box. Experiments that show a similar signal pattern to the current experiment can be searched for using the #Correlative Correlative Search function.

Advanced search features are available from the icons in the toolbar of the experiment panel and include:

Icon

Description

Open the experiment in a #Cortical Cortical Map Viewer, also where Intrinsic Signal Images (when available) will be displayed

Shortcut key to conduct a #Spatial Spatial Search from the point indicated by the cross hairs

Open the experiment in the 3-D Brain Explorer software

Open the experiment in a #High High Resolution Image Viewer

Open quantification of the signal in the #Experimental Experimental Detail page

Section Images Viewer

The section images viewer shows the 2-D fluorescence images in both the green (signal) channel and the red (autofluorescence) channel. Navigation (panning and zooming) through these images is achieved by using the on-screen navigation tools or using the #Keyboard Keyboard Commands.

This project utilizes extensive informatics processing and the informatics signal calculated by subtracting the background signal (segmentation images) can be viewed by clicking the icon.

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The cross-hairs on the Cortical Map indicate the location of the 2-D image from the experiment to the right. Navigation to other locations in the experiment is from either the on-screen navigation icons, or by double-clicking on the Cortical Map itself. Once a location has been chosen, the experimental ID, primary injection site, mouse line, position (in microns) and the location mapped to the reference atlas will show up in the left-hand corner of the screen. Clicking on the experimental ID link will take you to the #Experimental Experimental Detail Page. Only the Projection Density and Structures checkboxes will be available for experiments without ISI.

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The cross-hairs on the Cortical Map indicate the location of the 2-D image from the experiment to the right (not shown). Navigation to other locations in the experiment is from either the on-screen navigation icons, or by double-clicking on the Cortical Map itself. Once a location has been chosen, the experimental ID, primary injection site, mouse line, position (in microns) and the location mapped to the reference atlas will show up in the left-hand corner of the screen. Clicking on the experimental ID link will take you to the #Experimental Experimental Detail Page.

Experimental Detail Page

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  1. Injection Summary: This section includes a link to the #Cortical Cortical Map Viewer from the icon in the top right-hand corner and lists the experiment ID, primary and secondary injection structure(s), the coordinates of the injection, the mouse strain, tracer type and the calculated injection summary (%) for the rAAV injection and the CAV injection (where appropriate). If the experiment was targeted stereotaxically, the coordinates are from a registration point (typically Bregma) in the anterior/posterior, dorsal/ventral, medial/lateral orientations and the angle of injection (AP, ML, DV, <). If the experiment was targeted using ISI, the coordinates will read "ISI(0, 0, DV, <)" indicating the depth and angle of injection (see Overview whitepaper in Documentation). If the experiment shown is from a transgenic line, you will also have a description of the infected cells and a link to the Transgenic Characterization of that line.
  2. Projection Density Image Viewer: This viewer offers a rotating preview of the projection signal in 3 dimensions. Click the "View in 3D" link to view the experiment in the Brain Explorer software.
  3. Section Images Viewer The Section Images viewer allows you to browse the experiment in 2-D. You can scroll through thumbnails of each section, zooming in or out and panning through areas of interest.
  4. Histogram: This section illustrates the quantified signal in each structure either by projection volume (mm3) or by projection density (fraction of area occupied by signal compared to the whole structure). Toggle the two representations of the data using the drop down menu at the top of the histogram. The selected structure ontology can be expanded or collapsed and the number of structures shown can be changed using the threshold slider bar at the top of the histogram. When you click on a structure in the histogram, you will be taken to that area of the brain in the 3-D and 2-D image viewers. A red cross-hair pinpoints the center of that structure in each of the image viewers.

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To view an overlay of each of the selected experiments in the Experiment Image Viewer, click on the "#Composite Composite Projection Viewer" in the title bar.

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Control

Function

Select between raw data and projection segmentation images (See Informatics paper in the Documentation tab)

Adjust image controls

View all images in this experiment in a #Contact Contact Sheet Viewer

Display image in a #High High Resolution Image Viewer

Synchronize all other section image viewers on the page that support synchronization to the currently selected image

Close the Section Images viewer

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  1. Toggle between the individual image viewers and the composite viewer
  2. Add the coronal or sagittal reference atlas (will display below the Composite View) or change the number of columns (from the "gear")
  3. The #Composite Composite View. Clicking the "+" in the top left-hand corner will open up images of each experiment
  4. Display reference data such as the annotated reference atlas or histochemical stains that was already in your viewing cart

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Double-clicking on individual images on the contact sheet will launch a #High High Resolution Image Viewer.

High Resolution Image Viewer

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