Detect cell boundaries based on ssDNA images

The following tutorial descibes a simple demo example for cell segmentation pipeline based on nuclei staining image. The core function was built on cellprofiler which you can refer to CellProfiler as a Python package

import sys
sys.path.append('../../')

import cv2

%matplotlib inline
import matplotlib.pyplot as plt

we have include a demo image file for your testing, you can find with name ‘demo.tif’

image = cv2.imread('../../../WACCA/cellsegmentation/demo.tif')
plt.imshow(image)

<matplotlib.image.AxesImage at 0x14bb538e0>

import modules for image processing and cell object detection

import objseg

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
Cell In[5], line 1
----> 1 import objseg

ModuleNotFoundError: No module named 'objseg'

using clahe method to enhancing image with two iteration

image = objseg.clahe(image, iter=2, return_gray=True)
plt.imshow(image, cmap='binary_r')

<matplotlib.image.AxesImage at 0x2609f25f9a0>

In the enhanced image, cell nuclei in dark region were brighten to promote the detection of objects. Now starting the segmentation with cellprofiler.

image

x = image[:,:]

x

convert the image ndarray from rgb to gray

cell_mask, cell_boundary, img_boundary = objseg.pycellprofiler(
    x, return_image=True,)

***Error: ConfigBase.Write(): argument 2 has unexpected type 'WindowsPath'

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
d:\CodeSpace\4D-BioReconX\Preprocess\cellsegmentation\cell-segmente-on-ssDNA.ipynb Cell 15 line 1
----> <a href='vscode-notebook-cell:/d%3A/CodeSpace/4D-BioReconX/Preprocess/cellsegmentation/cell-segmente-on-ssDNA.ipynb#X22sZmlsZQ%3D%3D?line=0'>1</a> cell_mask, cell_boundary, img_boundary = objseg.pycellprofiler(
      <a href='vscode-notebook-cell:/d%3A/CodeSpace/4D-BioReconX/Preprocess/cellsegmentation/cell-segmente-on-ssDNA.ipynb#X22sZmlsZQ%3D%3D?line=1'>2</a>     x, return_image=True,)

TypeError: cannot unpack non-iterable NoneType object

image

plt.imshow(img_boundary)

except the returned numpy array of cell_mask and cell_boundary,

Reference:

[1] CellProfiler as a Python package