Multi-class tile import?
andreped opened this issue · 4 comments
The current tileImport script does not support multiclass tiles, that is produced prediction tiles generated from MIB by a trained multi-class model.
It is possible to import predictions from MIB to QuPath by predicting on the full WSI in MIB which produces a stitched prediction image, which can be imported in QuPath using the importStitchedTIFfromMIBscript, similarly as done for FastPathology. And therefore, for the full pipeline a tile importer is not critical for using our pipeline.
However, there are scenarios where having a tile importer is beneficial over the other alternative, for instance if one only wishes to run prediction on a smaller region of the WSI (based on segmentations in QuPath) - which can be especially helpful if the image is extremely large. This can make inference a lot faster.
It is possible to do such a workflow in FastPathology, given that you provide the region of interest to run inference on. However, no such method has been made easily accessible. It would also require annotations or a model that can produce these ROI segmentation to use as a preprocessing step for the next patch-wise model.
Therefore, having multi-class support for the tile importer could be a valuable feature.
I've just created a tutorial on how to do multiclass import on the WSI-level here: #10
In some rare cases one would ideally also like to be able to import multiclass predictions from DeepMIB from exported patches from QuPath, but the current WSI-prediction approach will suffice in most cases I think.