Tutorial 122 - Segmenting 3D datasets using 3D U-Net

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ZEISS arivis

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what a nice 3d modeling wonderfull lecture

zulfiqarali-zqrg

Thank you for your wonderful lectures helping me understand deeper

sjchodavid

Thank you for your video. What happen to the patch that only have background when you do inferring? presume your big image may have area where patch does not cover object of interest. Can the false positive happen? If so, should I put the non-object patch in the training set ? Thank you

kenny_tukin

That was a great lecture. One thing that confuses me, as you have 264 images stacked and mask for each image. However, I have 475 cases, each consist of 512 images and one mask for the whole 512 stacked images. Means a total of 475 mask. How I should approach this type scenario?

shahidAhmad

Dear Sreeni, I have nifti files and need to use nibabel package to read them and I think patchify doesn't work with this library. Do you have any advice on how to do patchify with other image formats than tiff ?

EkaterinaGolubeva-prih

Thanks a lot.
When I want to apply 3D Unet segmentation, what were Dataset that I need as input? How can I get mask image

dhaferalhajim

hey sreeni, do you work for ZEISS? Are you located in Germany and live here?

tonihullzer

Dear Sir, I am facing a typical problem in 3D segmentation. I have a set of NIFTY volumes, I am unable to use your code because stacking is increasing the tupple dimension to 6 from 5. Also, do you have this 3D code for lower version of tensorflow? (Currently stuck with tensorflow 2.4.0 and cannot upgrade it due to other reasons) ANy lead will be very helpful.

clueless

very interesting and important concept. Do you think that we can use this method to visualize the vessel around the nodule in CT-image is it work with ? if i have a 2 D CT? Thanks

JwanKAlwan

Thank you for your wonderful lecture, I have 10 subjects and each subject consist of 200 slices in shape 512*512*200. What will be the input dimensions of this data for the 3D Unet?

hamideandevari

Hi, it's a helpful and informative one. My dataset is comprised of nifti (.nii.gz) files. Please advise, how can I convert those into tif stack? Or i can directly feed them into the model for training? Thanks in advance.

mehnaztabassum

After converting from 2d to 3d I am founding this error. Solve this first and let me know. Otherwise you are learning wrong.
A `Concatenate` layer requires inputs with matching shapes except for the concat axis. Got inputs shapes: [(None, 512, 512, 6, 2), (None, 512, 256, 3, 1)]

al-akhirnayan

Hello, I have a 3D seismic data and actually want to try 3D-Unet

obasoroolakunle

Really cool! Im going to try this out to look at distribution of 2 specific cell organelles that I stained in immunofluorescence z stacks. In the end you are mentioning that it is possible to make measurements about volume and distribution of the segments. Would you be able to give me a hint on how to do that? Than you for all your content !

louisebuijs

how can I use APEER for visualizing segmented images?

mohamedomar-rpkz

And maybe how to determine cnn kernels before training process.

mohammadaghili

Hello. Can you please make a video for pixel classification of an image.

mohammadaghili

How do I convert .nii into .tif? Thanks

aqilahmohamad

Tutorial 122 - Segmenting 3D datasets using 3D U-Net

Tutorial 122 - Segmenting 3D datasets using 3D U-Net

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