How to know which transforms to apply, and what parameters to put

[ghost]

Hello,

I'm trying to segment zebrafish embryos with MONAI, but this is what I get. I think the main problem is how I transform the data.

What tranforms do you think I can use to fix this?

These are the tranforms I currently have:

train_transforms = Compose(
[
LoadImaged(keys=["vol", "seg"]),
EnsureChannelFirstD(keys=["vol", "seg"]),
Spacingd(keys=["vol", "seg"], pixdim=pixdim, mode=("bilinear", "nearest")),
Orientationd(keys=["vol", "seg"], axcodes="RAS"),
ScaleIntensityRanged(keys=["vol"], a_min=a_min, a_max=a_max, b_min=0.0, b_max=1.0, clip=True),
CropForegroundd(keys=["vol", "seg"], source_key="vol"),
Resized(keys=["vol", "seg"], spatial_size=spatial_size),
ToTensord(keys=["vol", "seg"]),
]
)
val_transforms = Compose(
[
LoadImaged(keys=["vol", "seg"]),
EnsureChannelFirstD(keys=["vol", "seg"]),
Spacingd(keys=["vol", "seg"], pixdim=pixdim, mode=("bilinear", "nearest")),
Orientationd(keys=["vol", "seg"], axcodes="RAS"),
ScaleIntensityRanged(keys=["vol"], a_min=a_min, a_max=a_max, b_min=0.0, b_max=1.0, clip=True),
CropForegroundd(keys=['vol', 'seg'], source_key='vol'),
Resized(keys=["vol", "seg"], spatial_size=spatial_size),
ToTensord(keys=["vol", "seg"]),
]
)

This is the results I have:

[KumoLiu]

Hi @bintadkr,

Generally, the selection of transformations in MONAI typically varies greatly depending on the specific task at hand. Although I can't pinpoint the issue directly from you code, I recommend diligently reviewing the output of each transformation. BTW, it's noteworthy that the image seems almost separable by a simple thresholding.

Hope it helps.
Thanks.