STimage-1K4M

Check spot location

We manually check the spot location on each slide. The processed coodinate file include yaxis, xaxis and the radius for each spot.

import sys
from typing import List,Dict
import pandas as pd
from PIL import Image
import pandas as pd
import matplotlib.pyplot as plt

Image.MAX_IMAGE_PIXELS = 3080000000000000000000000000000000000


# check the coordinate of the spot on the slide

def check_image_all(path,slide):
    temp_image = Image.open(f'{path}/image/{slide}.png')
    temp_image = temp_image.convert('RGB')
    coord = pd.read_csv(f'{path}/coord/{slide}_coord.csv')
    r = coord.r[0] # radius
    plt.clf()
    plt.imshow(temp_image)
    for i in range(len(coord.index)):
        yaxis = coord.yaxis[i]
        xaxis = coord.xaxis[i]
        plt.plot([xaxis-r,xaxis+r],[yaxis-r,yaxis-r],c='lime',alpha=0.5)
        plt.plot([xaxis-r,xaxis+r],[yaxis+r,yaxis+r],c='lime',alpha=0.5)
        plt.plot([xaxis-r,xaxis-r],[yaxis-r,yaxis+r],c='lime',alpha=0.5)
        plt.plot([xaxis+r,xaxis+r],[yaxis-r,yaxis+r],c='lime',alpha=0.5)
    # crop plt
    plt.axis('off')
    plt.axis([coord.xaxis.min()-r*2,coord.xaxis.max()+r*2,coord.yaxis.max()+r*2,coord.yaxis.min()-r*2])
    plt.savefig(f'./check_image_all/{slide}.png',dpi=100,bbox_inches='tight',pad_inches = 0)


meta = pd.read_csv('meta_all_gene.csv',sep='\t')

for index in range(len(meta)):
    slide = meta.slide[index]
    tech = meta.tech[index]
    # set your directory to downloaded STimage-1K4M
    path=f'./{tech}/'
    check_image_all(path,slide)
Search