voxelmorph
I ran voxelmorph on affine transformed zebra fish data! I used this tutorial https://www.kaggle.com/adalca/learn2reg/data The notebook is here https://github.com/mariakesa/Neural-Data-Analysis/blob/master/ZebraFish/Registration/voxelmorph_notebook.ipynb I had to change the code a little bit. It had a deprecated tf.Dimension variable in the utils file.
It seems to work!
It looks like it can handle very complex deformations.
Thinks I don't understand:
1. I had to resize the image to be in the same range as the tutorial. I don't understand how I should chnage this cell and why it has so many dimensions (4). What is nb_enc and nb_dec?
2. I don't understand how to input a single reference image for alignment.
3. I should really dig into the library and see how the algorithm works:-) Fortunately it uses Keras which is super comfy!
Anyway, I like it so far:-)
It seems to work!
It looks like it can handle very complex deformations.
Thinks I don't understand:
1. I had to resize the image to be in the same range as the tutorial. I don't understand how I should chnage this cell and why it has so many dimensions (4). What is nb_enc and nb_dec?
ndims = 2 vol_shape = x_train.shape[1:] nb_enc_features = [32, 32, 32, 32] nb_dec_features = [32, 32, 32, 32, 32, 16]
2. I don't understand how to input a single reference image for alignment.
3. I should really dig into the library and see how the algorithm works:-) Fortunately it uses Keras which is super comfy!
Anyway, I like it so far:-)
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