Mapping experiments to/from the atlas

Purpose

Once you have aligned (registered) your brain images to a brain atlas using tools to Register sections or Register volume, you can map data, such as markers for detected cells and contours that designate specific brain regions to obtain quantitative information about where the data are located.

The following tools provide the ability to bidirectionally map experimental and atlas information:

Map Experiment to Atlas maps experimental data (markers and 2D contours) into the common reference space of the brain atlas used for the registration.

The output is useful for quantitative comparisons between individual brains and for sharing data among different researchers and laboratories.

Map Atlas to Experiment maps selected anatomic brain regions from the atlas onto the experiment and generates contours around the regions.

This is designed to enable users to automatically identify and delineate regions in the experiment and for quantitative analyses within the experimental image(s).

See also the Analysis page for other options.

Map Experiment to Atlas

  1. Click Map Experiment to atlas on the Registration ribbon.

    The Map Experimental Data to Atlas window will open.

  2. Choose options for mapping and output of your data:

    If you have not already saved your data file, you will be prompted to do so. Enter a name for the file, click Browse and indicate where to save it. Note that your mapping results will be saved with the same base filename.

    Experiment options

    Planes: Click All to include all registered experimental image-planes or type in the range of image planes to include in the mapping.

    Brain regions: Choose the anatomic regions to include in your analysis:

    • Map to all brain regions: Maps to all brain regions in the atlas

    • Map to selected brain regions: Maps to brain regions that are displayed onscreen

    • Map to brain regions in group: If you set up groups of brain regions using the Atlas Ontology tools, they are listed in the drop-down menu. Click to select a group for mapping.

    Output Options

    • Include atlas images: Check to include images of the atlas region in the results

    • Report marker coordinates: Include the XYZ positions of markers in the coordinate space of both the experimental and atlas brains. Brain regions of markers are also reported.

    • Report number of markers per brain region: A summary report is created with the number of markers and contours per brain region.

      • Partition markers by plane: Check to include the image-plane information in the report

    • Jitter marker positions: Jittering the marker positions reduces the appearance of banding in results by slightly shifting marker positions along the sectioning axis.

      • Recommended for analyses of sectioned tissue

      • Not recommended for intact-tissue analyses

    • Marker intensity sampling region: When measuring the intensity of marked regions, you can specify the size of the window used to calculate marker intensity.

      Marker-intensity is the center-weighted average of intensity in the specified window.

  3. Click Begin to run the analysis.

    A window will open to tell you that the analysis is complete.

    Results

    When the analysis is complete, two types of data files are generated (.xml and .csv) in the output folder (same folder as .xml data file). Note that your mapping results will be saved with the same base filename.

    Successive analysis runs will overwrite the existing results files with new data. To save existing results files, alter the file names accordingly.

    • .xml: This is the standard saved data file that contains all experimental data: images, transforms, markers, and contours. This file will be created if the file had not been previously. If the file was already created, it will be updated.

    • _output.xml: Contains the atlas image volumes that you registered your experiment to so you can view the markers and contours in the atlas-ccordinate space. You can open this file in NeuroInfo and view your results.

      You may want to view the _output.xml file in the 3D Visualization window.

    • _points.csv: Contains the XYZ locations of each marker in both the experimental coordinate space and the atlas coordinate space. The strength of each marker by channel is also recorded in this files.

    • _summary.csv: The total marker count and average strength by channel are listed for each structure.

      Note that Strength is a relative intensity measure; it’s a weighted average of how much brighter the center of the detected object is from its surroundings. The value is normalized across scales; larger objects pull the weighted average from a wider area, but the responses are normalized to be comparable across scales.

    Learn more about coordinate spaces in NeuroInfo

Map Atlas to Experiment

  1. Click Map atlas to Experiment on the Registration ribbon.

    The Map Atlas to Experiment window will open.

  2. Choose options for mapping and output of your data:

    If you have not already saved your data file, you will be prompted to do so. Enter a name for the file, click Browse and indicate where to save it. Note that your mapping results will be saved with the same base filename.

    Experiment options

    Planes: Click All to include all experimental image-planes or type in the range of image planes to include in the mapping.

    Brain regions: Choose the anatomic regions to include in your analysis

    Map selected brain regions: Brain regions that are displayed onscreen are mapped

    Map brain regions in selected group: If you set up groups of brain regions using the Atlas Ontology tools, they are listed in the drop-down menu. Click to select a group for mapping.

    Output Options

    • Separate contours by left and right hemispheres: Right and left contours are reported for brain regions that cross the mid-sagittal plane.

    • Replace existing contours: Check the box to replace previously created contours when generating results. This is helpful if you want to evaluate the effects of different registration transforms on your results.

    • Contour detail: Use the slider to set the level of detail (number of points) used to draw contours.

  3. Click Begin to run the analysis.

    A window will open to tell you that the analysis is complete.

    Save your data file with the mapped brain regions if desired.