如何使用Python / OpenCV从医学图像中分割单个细胞？

Question

So I am trying to segment individual cells from a loaded image using Python/OpenCV. My code currently is able to mask the cells, but I would like to segment individual cells and save them as separate images.

So the output would be one of those single cells you see in the above (purposes for downstream use with 2D convnet)

img_dir = '/path'
img = cv2.imread(img_dir, 0)
plt.imshow(img, cmap = 'gray', interpolation = 'bicubic') # swap hot 
for gray

# draw a contour image with fixed threshold 50
fig = plt.figure()
ax = fig.add_subplot(111)
ax.contourf(img, levels=[0, 10, 20, 30,  40, 50, 60, 70, 80, 120], 
colors='k')
plt.show()

res = cv2.resize(img,None,fx=0.5, fy=0.5, interpolation = 
cv2.INTER_CUBIC)

Answer 1

Actually in this problem, segmentation is the process of separating the cells from the background which you already accomplished.

Being left with a binary image you have to perform a blob detection. After optionally filtering out everything that is of unwanted size or shape you are left with a list of blobs, each representing a cell I guess.

http://docs.opencv.org/trunk/dd/d49/tutorial_py_contour_features.html

https://www.learnopencv.com/blob-detection-using-opencv-python-c/

You then compute the so bounding rect of each of those blobs and use that rectangle to create a roi to crop the subimages.

How to crop an image in OpenCV using Python