File Exchange > Data Analysis >    Brain Atlas Analyzer

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Analyze images of brain, define multiple ROIs for each desired image in the collection, and then extract stats.

Screen Shot and Video:


This app can help neuroscientists to accelerate the progress of Brain Atlas Map analysis.

The app was developed in collaboration with Manuel Castro-Alamancos, a Professor at UConn School of Medicine (


Download the opx file from this page and then drag and drop it onto Origin workspace, or click the Add Apps button to open the App Center and then search for &ldquoBrain&rdquo to download and install.

Note that this tool requires the Pro version.


Click on this app icon, and a small toolbar will appear in the center of Origin workspace. There are several buttons on the toolbar:

1. Import Image Slices: import image files and slices them into a matrix window.

When the Import Image Slices button is clicked, a blank workbook appears with two buttons at the top.

Click the Select Images button to browse to the folder and select your images. We offer you a few options to cut the original image into parts:

  • Offset: Specify how much to offset each section from the bottom. This is useful if the sections are offset from the top of the image.
  • Overlap: Specify how much the cut of each section should overlap. This is useful when sections are not placed evenly on the slide.
  • Number of Rows: Specify the number of rows of sections in the image.
  • Number of Columns: Specify the number of columns of sections in the image.

Note: Once you apply the settings, Origin will fill in the values on the sheet but you can still change the values as needed

Click the Import Images button to arrange the images and name the generated matrix sheets:

  • Order: Specify the arrangement of your sections on the slide
  • Scale: Specify whether to reduce or increase the size of the images
  • Rotate: Specify whether to rotate the orientation
  • Sheet Specification: Specify the section thickness and the value of the atlas to which your first section corresponds. Origin will use these numbers as the names of the matrix sheets it creates later


2. Insert Brain Atlas(SVG): import SVG into the matrix window

Click the Insert brain atlas button to browse the folder and select *.svg file :

  • Start SVG: Specify the first atlas
  • Starting Images: Specify the first section
  • RBG to Acronym Map: Specify the JSON files that define the acronym map of the atlas
  • Acronym to Fullname Map: Specify the JSON files that define the full name of the acronym map
  • SVG Offset Index: Specify how many images of the atlas correspond to the interval between the sections
  • Transparency: Adjust the transparency of the atlas, which allows you to see the overlay of the atlas on the matrix image.

Note: For the SVG files, it is required that the names should contain number suffix, Origin will calculate the subsequent SVG file name by the offset specified in the dialog. Once you click the OK button, the atlas SVG will be superimposed on the matrix and this will be repeated for all the other matrices.


3. Shift Left: shift the SVG one step(matrix) leftward.

4. Shift Right: shift the SVG one step(matrix) rightward.

These buttons help you to move the atlas image until you find an atlas image that best matches to the current section. A click on the Shift Left button will move the SVGs one sheet leftward, and A click on the Shift Right button will move the SVGs one sheet rightward.


5. Apply the Current Size and Position to All: apply the resize/position/rotate of the SVG in the active sheet to all other matrix sheets

Click anywhere on the matrix image, and the borderline of the atlas will appear. You can resize and rotate the borderline to match the size of the section. When you are satisfied, you can click the Apply the Current Size and Position to All button to apply the adjustment to all atlases on the matrix sheets.


6. Show or Hide Stroke: toggle show/hide status (3 modes) of the SVG

Click the Show or Hide Stroke button to toggle the status: show atlas, hide atlas, or show nuclei definitions.


7. Create ROI: create ROI for SVG paths

Click the Create ROI button to open a dialog listing all the nuclei, then select one or more nuclei of interested in from the Name drop-down list. When you click the OK button, you will see the red ROIs being created.

After the ROIs are created, you can perform an intensity analysis on them by right-clicking on the red ROIs and selecting Intensity Profile:

  • Profile on: Decide whether to perform the analysis on active ROI or on all ROIs
  • Statistics: Specify the quantities you want to obtain
  • Weighted ROI: Decide whether to calculate the percentage of ROI overlapped one pixel
  • RGB Profile: Decide whether to output the RGB profile separately


8. Update Transparency: change SVG transparency on the matrix

If you need to change the transparency of the atlas during the analysis, click the Update Transparency button


9. Overlay of 2 ROIs: Calculate the percentage of overlap between a manually drawn ROI and the ROI created by this app.

First, you should use the Draw tool, usually located below the Line and Text tools on the left side of Origin workspace, to manually draw an ROI on the matrix, then click Overlay of 2 ROIs button, Origin will help to calculate the overlap in pixels between the drawn ROI and the ROI created by this app.


Reviews and Comments:
05/16/2023orrtimFantastic, thank you for supporting Neuroscientist.

05/09/2023OriginLabHi, yenjun0204
The app helps to overlay atlas on brain images but it does not include any atlas in it. Users need to prepare the atlas by themselves.

05/08/2023yenjun0204Will you plan to include the rat atlas later?

Thank you,

05/07/2023OriginLabHi yenjun0204,
We use that brain atlas of mice and human both in this app.

05/05/2023yenjun0204What kind of brain atlas is used in the app? Is it for rats, mice, or humans?