Tutorial 51 - What is image thresholding and segmentation?

[@nayo7888]

Excellent video. The explanations are so clear, even for someone without a background in microscopy.

[@familywu3869]

Thank you very much for your teaching, Professor. This is an excellent lecture series, and I have learned a lot from it. Thank you very much again for sharing your wisdom.

[@JarashanthSelvarajah]

Very informative and simplified.

[@martinkinisu7946]

Glad I found your tutorials! Could you explain what we would have to do to do this for all stacks in a Z-projection? Does the read in variable in that case have another index that keeps track of stack that we could access?

[@ZEISS_arivis]

Yes, absolutely. When you read in an image stack the numpy array includes extra dimension for the z position. For multidimensional tif images (e.g. z stack) please use tifffile library to read images. Also, for this method, you need to work with one slice in the stack at a time so when writing code you will have to keep this in mind.

[@martinkinisu7946]

@@ZEISS_arivis Thanks for the reply! all makes sense, but i'm curious whether we will be able to avoid overcounting nuclei present in multiple stacks?

[@sugandhasingh3833]

@@ZEISS_arivis Thanks for your reply

[@eitanas85]

Dear Professor, I am really enjoying and learning a lot from your lectures. I was wondering, Where can I get the images you use in your tutorial? Warm wishes, Eitan

[@sadafhajiha948]

Thanks alot for your informative and well-explained tutorials. I have a question. I read a DICOM file and then want to do the segmentation on it. My question is that how should I save the DICOM file I read as volumetric data, to be able to do segmentation and thresholding on it? I am asking you this question because I save itas png, and. now I am not able to even have histogram for it.

[@tymothylim6550]

Thank you very much for this video! It is very educational and well-explained :)

[@ZEISS_arivis]

You're very welcome!

[@JwanKAlwan]

Thanks dr. for your informative lecture. Please what should I used to segment irregular shapes in CT scan like tumour .what is the best technique

[@ZEISS_arivis]

Please follow our Deep learning videos on the topic of semantic segmentation (using Unet)

[@bhu-gyaan-vigyaan1194]

How can i can get your mentorship to learn python use for my project.

[@yunshunzhong4491]

Why the final image after OSTU is yellow and purple instead of black and white?

[@nirajanbekoju6380]

plt.imshow(image, cmap = 'gray')

[@yunshunzhong4491]

Thank you so much!

[@danielabatalha5434]

amazing videos. its sad people enjoy but dont like this rich job ;

[@ZEISS_arivis]

Thanks :)

[@radheshasa4642]

Hello Sir , May I know the ide used ??

[@ZEISS_arivis]

I use Spyder IDE that comes with Anaconda.

[@sugandhasingh3833]

how to apply lagrange interpolation method to image?

[@ZEISS_arivis]

I never found the need to use Lagrange interpolation for an image. But I do know that it is available in the scipy library. I am aware of this method to be a way of interpolating if you know the polynomial but I am not sure how you'd represent an image or image patches as a polynomial.

[@sugandhasingh3833]

@@ZEISS_arivis Thank You sir

[@sugandhasingh3833]

can you tell me which interpolation method can be applied in image?

[@ajaykumarswarna1552]

sir what is advantages and dis advantages

[@ZEISS_arivis]

Advantages and disadvantages of what? If you are inquiring about thresholding and segmentation then the simple answer is that thresholding is just a way of segmenting images.