PytorchConnectomics
diff --git a/‎tutorials/fiber.yaml‎ ‎tutorials/fiber_linghu26.yaml‎tutorials/fiber.yaml renamed to tutorials/fiber_linghu26.yaml
Lines changed: 6 additions & 8 deletions b/‎tutorials/fiber.yaml‎ ‎tutorials/fiber_linghu26.yaml‎tutorials/fiber.yaml renamed to tutorials/fiber_linghu26.yaml
Lines changed: 6 additions & 8 deletions
diff --git a/‎…ls/HYDRA_LV_FINETUNE_IMPROVEMENT_PLAN.md‎ ‎…sc/HYDRA_LV_FINETUNE_IMPROVEMENT_PLAN.md‎tutorials/HYDRA_LV_FINETUNE_IMPROVEMENT_PLAN.md renamed to tutorials/misc/HYDRA_LV_FINETUNE_IMPROVEMENT_PLAN.md b/‎…ls/HYDRA_LV_FINETUNE_IMPROVEMENT_PLAN.md‎ ‎…sc/HYDRA_LV_FINETUNE_IMPROVEMENT_PLAN.md‎tutorials/HYDRA_LV_FINETUNE_IMPROVEMENT_PLAN.md renamed to tutorials/misc/HYDRA_LV_FINETUNE_IMPROVEMENT_PLAN.md
diff --git a/‎tutorials/example_tile_metadata.json‎ ‎tutorials/misc/example_tile_metadata.json‎tutorials/example_tile_metadata.json renamed to tutorials/misc/example_tile_metadata.json b/‎tutorials/example_tile_metadata.json‎ ‎tutorials/misc/example_tile_metadata.json‎tutorials/example_tile_metadata.json renamed to tutorials/misc/example_tile_metadata.json
diff --git a/‎tutorials/hydra-lv-finetune.yaml‎ ‎tutorials/misc/hydra-lv-finetune.yaml‎tutorials/hydra-lv-finetune.yaml renamed to tutorials/misc/hydra-lv-finetune.yaml b/‎tutorials/hydra-lv-finetune.yaml‎ ‎tutorials/misc/hydra-lv-finetune.yaml‎tutorials/hydra-lv-finetune.yaml renamed to tutorials/misc/hydra-lv-finetune.yaml
diff --git a/‎tutorials/hydra-lv-finetune_v0.yaml‎ ‎tutorials/misc/hydra-lv-finetune_v0.yaml‎tutorials/hydra-lv-finetune_v0.yaml renamed to tutorials/misc/hydra-lv-finetune_v0.yaml b/‎tutorials/hydra-lv-finetune_v0.yaml‎ ‎tutorials/misc/hydra-lv-finetune_v0.yaml‎tutorials/hydra-lv-finetune_v0.yaml renamed to tutorials/misc/hydra-lv-finetune_v0.yaml
diff --git a/‎tutorials/hydra-lv.yaml‎ ‎tutorials/misc/hydra-lv.yaml‎tutorials/hydra-lv.yaml renamed to tutorials/misc/hydra-lv.yaml b/‎tutorials/hydra-lv.yaml‎ ‎tutorials/misc/hydra-lv.yaml‎tutorials/hydra-lv.yaml renamed to tutorials/misc/hydra-lv.yaml
diff --git a/‎tutorials/mito2dsem_nnunet.yaml‎ ‎tutorials/misc/mito_2dsem_seg.yaml‎tutorials/mito2dsem_nnunet.yaml renamed to tutorials/misc/mito_2dsem_seg.yaml b/‎tutorials/mito2dsem_nnunet.yaml‎ ‎tutorials/misc/mito_2dsem_seg.yaml‎tutorials/mito2dsem_nnunet.yaml renamed to tutorials/misc/mito_2dsem_seg.yaml
diff --git a/‎tutorials/tsai_axon.yaml‎ ‎tutorials/misc/tsai_axon.yaml‎tutorials/tsai_axon.yaml renamed to tutorials/misc/tsai_axon.yaml b/‎tutorials/tsai_axon.yaml‎ ‎tutorials/misc/tsai_axon.yaml‎tutorials/tsai_axon.yaml renamed to tutorials/misc/tsai_axon.yaml
diff --git a/‎tutorials/worm2d.yaml‎ ‎tutorials/misc/worm2d.yaml‎tutorials/worm2d.yaml renamed to tutorials/misc/worm2d.yaml b/‎tutorials/worm2d.yaml‎ ‎tutorials/misc/worm2d.yaml‎tutorials/worm2d.yaml renamed to tutorials/misc/worm2d.yaml
diff --git a/‎tutorials/zebrafish_neurons.yaml‎ ‎tutorials/misc/zebrafish_neurons.yaml‎tutorials/zebrafish_neurons.yaml renamed to tutorials/misc/zebrafish_neurons.yaml b/‎tutorials/zebrafish_neurons.yaml‎ ‎tutorials/misc/zebrafish_neurons.yaml‎tutorials/zebrafish_neurons.yaml renamed to tutorials/misc/zebrafish_neurons.yaml
@@ -225,17 +225,15 @@ monitor:
     threshold: 0.01
     divergence_threshold: 100.0
 
-# Inference - MONAI SlidingWindowInferer for fiber segmentation (based on barcode-R-Base.yaml)
-inference:
+test:
   data:
     # Test on all available volumes (matches barcode INFERENCE IMAGE_NAME)
-    # Note: test_path will be combined with these relative paths
-    test_path: "/projects/weilab/dataset/barcode/train_r2/"
-    test_image: ["DG_LZ58/0702-2-C4-DG-40X002_1-raw.tif"]
-    test_label: ["DG_LZ58/0702-2-C4-DG-40X002_1-mask.tif"]
+    test_image: ["/projects/weilab/dataset/barcode/train_r2/DG_LZ58/0702-2-C4-DG-40X002_1-raw.tif"]
+    test_label: ["/projects/weilab/dataset/barcode/train_r2/DG_LZ58/0702-2-C4-DG-40X002_1-mask.tif"]
     test_resolution: [40, 16, 16]   # Isotropic resolution
-    # Output filename (auto-pathed based on the checkpoint folder)
-    output_name: DG_train.h5
+
+# Inference - MONAI SlidingWindowInferer for fiber segmentation (based on barcode-R-Base.yaml)
+inference:
 
   # MONAI SlidingWindowInferer parameters
   sliding_window: