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Experiments related to finding the source of tiling artifacts in the segmentation pipelines based on the sliding window inference

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kreshuklab/no_tiling_artifacts

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no_tiling_artifacts

Sliding window inference

Tutorials

Experimental setups organoids

Name norm layer track_running_stats whole vol percentile norm tile-wise percentile norm intensity augm dropout use running stats in training
setup_01 InstanceNorm True yes no no no no
setup_02 InstanceNorm True yes yes no no no
setup_03 InstanceNorm False yes no no no no
setup_04 InstanceNorm False yes yes no no no
setup_05 InstanceNorm True yes no no no no
setup_06 BatchRenorm True yes no no no no
setup_07 NoNorm False yes no no no no

Experimental setups plants

Name norm layer track_running_stats whole vol percentile norm tile-wise percentile norm intensity augm dropout use running stats in training
setup_01 InstanceNorm True yes no no no no
setup_02 InstanceNorm True yes yes no no no
setup_03 InstanceNorm False yes no no no no
setup_04 InstanceNorm False yes yes no no no
setup_05 InstanceNorm True yes no no no no
setup_06 BatchRenorm True yes no no no no
setup_07 NoNorm False yes no no no no

Experimental setups UNETR

(same for all 3 datasets)

Name norm layer track_running_stats whole vol percentile norm tile-wise percentile norm intensity augm dropout use running stats in training
setup_01 InstanceNorm False yes no no no no
setup_02 InstanceNorm True yes no no no no
setup_03 BatchRenorm True yes no no no no
setup_04 NoNorm False yes no no no no

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Experiments related to finding the source of tiling artifacts in the segmentation pipelines based on the sliding window inference

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