Scalebar conversion

[alissa777]

Hi

My name is Alissa. Sorry for bother you. It's me agian. I use ImageJ to measure the scalebar in pixel.

As the image 1 shown, this 20nm scalebar was converted to distance in pixels of 83.5. I think its right. However, I dont know how to input this figure into the code to make the tool process smoothly.

Could I input this 83.5 manually into the original code?

Thank you!

[by256]

Hi Alissa,

You can simply calculate the conversion as 20/83.5. This will be in units of nm/px. Change the line

conversion = data.scalebar.conversion

to

conversion = 20 / 83.5.

Then change the lines

sizes = sizes / conversion sizes = sizes * 1e-9

to

sizes = sizes * conversion

Since sizes was originally in units of px, and conversion is in units of nm/px, multiplying the two gives you the result in nm.

Hope this helps. Let me know if this solves your problem so that I can close the issue.

Batuhan

[alissa777]

Hi Batuhan,

Thank you for your reply.

I tried to follow the instruction and changed the these lines. However I got same error.

I was confused that I should just input the line: conversion = 20 / 83.5 Or I should calculate it by myself and input the results, so I tried both.

But the errors I got were same, as figure 2 shown.

Thank you again for helping me. Alissa

[by256]

You're trying to draw scalebar contours which do not exist onto the image. Because imagedataextractor's scalebar detection failed, data.scalebar.scalebar_contour is None, which is why you're getting this error. Remove these lines

sb_image = cv2.drawContours(image, [data.scalebar.scalebar_contour], 0, (0, 255, 0), 2)

plt.imshow(sb_image[700:, 700:]) plt.axis('off') plt.show()

[alissa777]

Thank you. It succeeded! I got output results. And there are some lines as well. I wonder it could affect the result or not.

Thank you for your replying! Take care!