HeatMap

HeatMap

This protocol describes how to map mouse anatomical data (or anything that can be drawn) onto a map using the HeatMap program. The HeatMap program was developed at the Center for Neurodegenerative Disease Research (CNDR) at the University of Pennsylvania. Any requests for use of the software should be directed to the CNDR.

HeatMap Generation

Very simply, to generate a new heatmap image in the software, you will load files using the radio buttons from left to right.

1. Load Image 

2. Load Descriptor

3. Load Scale

4. Load Data File

5. Upon loading the data file, you will generate an image. You can then, Save Images. The image will save in the location of the original image template.
 

Images

The images interpreted by this program are in .png format and use gray-scale values to map a corresponding region with a corresponding value along a 0-3 scale. Original images can be generated in Adobe Illustrator and subsequently saved as a high-resolution .png file.

It is important to note that each grayscale value will correspond to a different region. Therefore, when generating or updating images, make sure that no two regions contain the same grayscale value.

Assigning grayscale values

Grayscale values can be assigned by changing the color of an object in Adobe Illustrator. You do not need to know the actual value when assigning them. You will determine this in HeatMap.
Once you have generated an image, save a low resolution copy for testing grayscale values. Open HeatMap and Load Image your low-resolution image. Press Base Color Mode. A text box will pop up on the right. When you left click a region, it will display the gray value of those regions. The value can then be copied and pasted in the “Descriptor” cell corresponding to that region. After generating a new image, test the correct assignment of values to the corresponding region.
 

Descriptors

Descriptors are simple, CSV files with the region of interest listed in the first column and the gray value of the corresponding region listed in the second column. The gray values can be determined using the method described above. It is critical that the regions here match the regions in your data file. Otherwise the assignment of values in the final image will be incorrect.

Scales

Scales allow the assignment of numbers from 0-3 to a color scale. The scale is 737 x 32 px (though the exact size may not be critical). To generate a new scale in Adobe Photoshop, generate a new

image of the correct size. Use the gradient tool to make the scale you would like to use. It may also be useful to add a small gray bar at the left end of the bar so that zero values are assigned as gray, instead of a color. Save the scale as a high-resolution .png file.

Data Files

Data files are another simple CSV file with the figure image to be generated listed in the first column, the region number in the second column and the values you have generated in the third column. You will have to generate separate data files for each image you would like to create. Keep in mind that numbers 0-3 will be evenly assigned along the color scale you generated. Therefore, any values you have generated that are not in this range will need to be converted to this scale before putting them into HeatMap.

Base Color Mode

This radio button is used as described in the image section to find assigned gray values in any image.

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