About mouse olfactory bulb dataset

[cquzys]

Hi author:
I obtained the mouse olfactory bulb dataset obeyed the address: https://www.spatialresearch.org/resources-published-datasets/doi-10-1126science-aaf2403/.
However, I didn't understand how to plot the data on top of the HE image. For example, the instructions in section Alignments: "you can either rescale the image to the array size (1,1,33,35) or transform the spot coordinates to image pixel coordinates using these alignment 3×3 matrices:"

Can you tell me how to plot the data on the top of the HE image easily?

Thanks

[ludvb]

Hi,

Here is an example showing how to use the alignment matrix to convert the array coordinates in the count file to pixel coordinates:

import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from imageio import imread

data = pd.read_csv("./Rep1_MOB_count_matrix-1.tsv", sep="\t", index_col=0)
alignment_matrix = np.loadtxt("./Rep1_MOB_transformation.txt")
image = imread("./HE_Rep1_MOB.jpg")

array_coords = np.array([[float(a) for a in x.split('x')] for x in data.index])
array_coords_h = np.concatenate([array_coords, np.ones((array_coords.shape[0], 1))], 1)
pixel_coords_h = array_coords_h @ alignment_matrix.reshape(3,3)
pixel_coords = pixel_coords_h[:, :2]

plt.imshow(image)
plt.scatter(pixel_coords[:, 0], pixel_coords[:, 1])
plt.show()

Let me know if you have any questions!

[Yizhi-Zhang]

Hi, @ludvb

Thank you for your interesting work.

I encountered some issues when applying XFuse to the mouse olfactory bulb dataset. Could you please advise on how to modify my config.toml file and could you provide a reference configuration file?

Thank you very much!