Digitizing heatmap image

[deepa]

Hi,

I'd like to digitize a heatmap

Panel D in this source: https://www.ncbi.nlm.nih.gov/pmc/article...figure/F1/

I'm not sure what's the right way to proceed. Any suggestions?

Thanks

[scidam]

If this is the only one figure you need to digitize, I would suggest to do it manually.
What would be an algorithm, if you wrote this program using Python.
1) Read the figure using sickit-image or PIL, and clasterize colors (find all different colors that
are used); Probably, you'll need make some rotation adjustment of the picture first.
2) Find centers for the clusters with the same color and build a matrix of colors A[i,j] (i num of row, j num of column in the chart);
3) map colors to names, column names and row names respectively; this probably is to be done manually, e.g. {'color': 'row_name1', ...etc}
4) The only last step is to define mapping between row/column number and name. That's all.

I suspect that it take no more than 20 minutes to digitize the chart manually.

[deepa]

Hello,

Thanks a lot for the response. I prefer to digitize using python, I have to use this approach for processing other images too.

From what you suggested, I tried the following

import cv2
from pprint import pprint


def read_as_digital(image, offset_x, offset_y):
    # grab the image dimensions
    h = image.shape[0]
    w = image.shape[1]
    print(h, w)
    pass


if __name__ == '__main__':

    image = cv2.imread('ip.jpg', 1)
    pprint(image)

    read_as_digital(image, [], [])

I could read the image as a matrix, but I don't know how to specify the beginning of the cells (corresponding to different subplots in panel D of the image) in the heatmap.

Also, could you please explain how this can be done and why this has to be done?
Any suggestions?