Overlapping patches and Sliding Window mechanism

[Aayush2003Gupta]

Hi!!
I had some questions regarding GaNDLF. I would be really grateful if I could get some help regarding them.

Does GaNDLF support overlapping patches or the sliding window mechanism during inference/training ?

Thanks a lot in advance!!!
Aayush Gupta

[sarthakpati]

Hi,

GaNDLF kind of supports this.

• For histology images [ref]: You can use the configuration parameters overlap_factor and read_type: sequential.
• For radiology images: This is a bit more complicated, and it is not possible (at least right now) to perform sliding window mechanism for patch extraction. You can use the queue parameters [ref] to kind of simulate this. Specifically, you can use q_samples_per_volume. Let's say your patch size for training is [128,128,128] and your total image size per modality is [240,240,155] with patch_sampler: uniform, you can use q_samples_per_volume: 5 to ensure the entire volume is captured (there will be overlap which you , though).

Hope this helps!