Python: Crop out area from image along borders
What functions (and how I should use them) should I use to crop out the center part of this image? I want to take just the less-dense parts, not the dense borders.
Thanks!
In the end, I want to either count the tiny circles/dots (cells) in the areas or calculate the area of the less-dense parts, outlined in the second image. I've done this before with ImageJ by tracing out the area by hand, but it is a really tedious process with lots of images.
I've currently looked at Scipy, but they are big and I don't really know how to approach this. If someone would point me in the right direction, that would be great!
It would take me a bit longer to do in Python, but I tried a few ideas just on the command-line with ImageMagick which is installed on most Linux distros and is available for free for macOS and Windows.
First, I trimmed your image to get rid of extraneous junk:
Then, the steps I did were:
- discard the alpha/transparency channel
- convert to greyscale as there is no useful colour information,
- normalised to stretch contrast and make all pixels in range 0-255,
- thresholded to find cells
- replaced each pixel by the mean of their surrounding 49x49 pixels (box blur)
- thresholded again at 90%
That command looks like this in Terminal/Command Prompt:
convert blobs.png -alpha off -colorspace gray -normalize -threshold 50% -statistic mean 49x49 -threshold 90% result.png
The result is:
If that approach looks promising for your other pictures we can work out a Python version pretty quickly, so let me know.
Of course, if you know other useful information about your image that could help improve things... maybe you know the density is always higher at the edges, for example.
In case anyone wants to see the intermediate steps, here is the image after grey scaling and normalising:
And here it is after blurring:
