Spotlight v2 segmentation-aware-loss

applications/dynacell/configs/benchmarks/virtual_staining/_internal/leaf/grouped/spotlight_v2_er_a549_denv__wave2s/eval_grouped.yaml

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+# @package _global_
+# Spotlight-v2 bucket spotlight_v2_er_a549_denv__wave2s (2 conditions). Auto-generated by
+# tools/generate_spotlight_v2_eval_configs.py from spotlight_v2_eval_roster.yaml; edit the roster, not this file.
+# save_dir / pred_cache_dir live under /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2
+# (never the canonical dirs the paper reads); the GT caches are the shared manifest
+# ones. Every pred_* artifact is forced.
+target_name: er
+compute_feature_metrics: true
+use_gpu: true
+io:
+  require_complete_cache: false
+runtime:
+  executor: serial
+  fov_workers: 1
+  threads_per_worker: auto
+force_recompute:
+  final_metrics: true
+  pred_masks: true
+  pred_cp: true
+  pred_dinov3: true
+  pred_dynaclr: true
+  pred_celldino: true
+  pred_morphem: true
+  pred_instances: true
+conditions:
+- name: fnet3d_vscyto3daug_v2__ipsc_trained__a549_denv
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-sec61b-denv
+      target: sec61b
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/er/fnet3d_vscyto3daug_v2/ipsc/a549__denv/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/er/fnet3d_vscyto3daug_v2/ipsc/a549__denv
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/er/fnet3d_vscyto3daug_v2/ipsc/a549__denv
+- name: fnet3d_vscyto3daug_v2_seed1__ipsc_trained__a549_denv
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-sec61b-denv
+      target: sec61b
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/er/fnet3d_vscyto3daug_v2_seed1/ipsc/a549__denv/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/er/fnet3d_vscyto3daug_v2_seed1/ipsc/a549__denv
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/er/fnet3d_vscyto3daug_v2_seed1/ipsc/a549__denv

applications/dynacell/configs/benchmarks/virtual_staining/_internal/leaf/grouped/spotlight_v2_er_a549_denv__wave2t/eval_grouped.yaml

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+# @package _global_
+# Spotlight-v2 bucket spotlight_v2_er_a549_denv__wave2t (1 conditions). Auto-generated by
+# tools/generate_spotlight_v2_eval_configs.py from spotlight_v2_eval_roster.yaml; edit the roster, not this file.
+# save_dir / pred_cache_dir live under /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2
+# (never the canonical dirs the paper reads); the GT caches are the shared manifest
+# ones. Every pred_* artifact is forced.
+target_name: er
+compute_feature_metrics: true
+use_gpu: true
+io:
+  require_complete_cache: false
+runtime:
+  executor: serial
+  fov_workers: 1
+  threads_per_worker: auto
+force_recompute:
+  final_metrics: true
+  pred_masks: true
+  pred_cp: true
+  pred_dinov3: true
+  pred_dynaclr: true
+  pred_celldino: true
+  pred_morphem: true
+  pred_instances: true
+conditions:
+- name: fnet3d_vscyto3daug_segaux__ipsc_trained__a549_denv
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-sec61b-denv
+      target: sec61b
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/er/fnet3d_vscyto3daug_segaux/ipsc/a549__denv/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/er/fnet3d_vscyto3daug_segaux/ipsc/a549__denv
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/er/fnet3d_vscyto3daug_segaux/ipsc/a549__denv

applications/dynacell/configs/benchmarks/virtual_staining/_internal/leaf/grouped/spotlight_v2_er_a549_denv__wave2x/eval_grouped.yaml

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+# @package _global_
+# Spotlight-v2 bucket spotlight_v2_er_a549_denv__wave2x (1 conditions). Auto-generated by
+# tools/generate_spotlight_v2_eval_configs.py from spotlight_v2_eval_roster.yaml; edit the roster, not this file.
+# save_dir / pred_cache_dir live under /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2
+# (never the canonical dirs the paper reads); the GT caches are the shared manifest
+# ones. Every pred_* artifact is forced.
+target_name: er
+compute_feature_metrics: true
+use_gpu: true
+io:
+  require_complete_cache: false
+runtime:
+  executor: serial
+  fov_workers: 1
+  threads_per_worker: auto
+force_recompute:
+  final_metrics: true
+  pred_masks: true
+  pred_cp: true
+  pred_dinov3: true
+  pred_dynaclr: true
+  pred_celldino: true
+  pred_morphem: true
+  pred_instances: true
+conditions:
+- name: fnet3d_vscyto3daug_segaux_sauna__ipsc_trained__a549_denv
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-sec61b-denv
+      target: sec61b
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/er/fnet3d_vscyto3daug_segaux_sauna/ipsc/a549__denv/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/er/fnet3d_vscyto3daug_segaux_sauna/ipsc/a549__denv
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/er/fnet3d_vscyto3daug_segaux_sauna/ipsc/a549__denv

applications/dynacell/configs/benchmarks/virtual_staining/_internal/leaf/grouped/spotlight_v2_er_a549_denv__wave3b/eval_grouped.yaml

@@ -0,0 +1,35 @@
+# @package _global_
+# Spotlight-v2 bucket spotlight_v2_er_a549_denv__wave3b (1 conditions). Auto-generated by
+# tools/generate_spotlight_v2_eval_configs.py from spotlight_v2_eval_roster.yaml; edit the roster, not this file.
+# save_dir / pred_cache_dir live under /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2
+# (never the canonical dirs the paper reads); the GT caches are the shared manifest
+# ones. Every pred_* artifact is forced.
+target_name: er
+compute_feature_metrics: true
+use_gpu: true
+io:
+  require_complete_cache: false
+runtime:
+  executor: serial
+  fov_workers: 1
+  threads_per_worker: auto
+force_recompute:
+  final_metrics: true
+  pred_masks: true
+  pred_cp: true
+  pred_dinov3: true
+  pred_dynaclr: true
+  pred_celldino: true
+  pred_morphem: true
+  pred_instances: true
+conditions:
+- name: fnet3d_vscyto3daug_segaux_cldice__ipsc_trained__a549_denv
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-sec61b-denv
+      target: sec61b
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/er/fnet3d_vscyto3daug_segaux_cldice/ipsc/a549__denv/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/er/fnet3d_vscyto3daug_segaux_cldice/ipsc/a549__denv
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/er/fnet3d_vscyto3daug_segaux_cldice/ipsc/a549__denv

applications/dynacell/configs/benchmarks/virtual_staining/_internal/leaf/grouped/spotlight_v2_er_a549_denv__wave3h/eval_grouped.yaml

@@ -0,0 +1,35 @@
+# @package _global_
+# Spotlight-v2 bucket spotlight_v2_er_a549_denv__wave3h (1 conditions). Auto-generated by
+# tools/generate_spotlight_v2_eval_configs.py from spotlight_v2_eval_roster.yaml; edit the roster, not this file.
+# save_dir / pred_cache_dir live under /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2
+# (never the canonical dirs the paper reads); the GT caches are the shared manifest
+# ones. Every pred_* artifact is forced.
+target_name: er
+compute_feature_metrics: true
+use_gpu: true
+io:
+  require_complete_cache: false
+runtime:
+  executor: serial
+  fov_workers: 1
+  threads_per_worker: auto
+force_recompute:
+  final_metrics: true
+  pred_masks: true
+  pred_cp: true
+  pred_dinov3: true
+  pred_dynaclr: true
+  pred_celldino: true
+  pred_morphem: true
+  pred_instances: true
+conditions:
+- name: fnet3d_vscyto3daug_segaux_seed1__ipsc_trained__a549_denv
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-sec61b-denv
+      target: sec61b
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/er/fnet3d_vscyto3daug_segaux_seed1/ipsc/a549__denv/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/er/fnet3d_vscyto3daug_segaux_seed1/ipsc/a549__denv
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/er/fnet3d_vscyto3daug_segaux_seed1/ipsc/a549__denv

applications/dynacell/configs/benchmarks/virtual_staining/_internal/leaf/grouped/spotlight_v2_er_a549_mock__wave2s/eval_grouped.yaml

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+# @package _global_
+# Spotlight-v2 bucket spotlight_v2_er_a549_mock__wave2s (2 conditions). Auto-generated by
+# tools/generate_spotlight_v2_eval_configs.py from spotlight_v2_eval_roster.yaml; edit the roster, not this file.
+# save_dir / pred_cache_dir live under /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2
+# (never the canonical dirs the paper reads); the GT caches are the shared manifest
+# ones. Every pred_* artifact is forced.
+target_name: er
+compute_feature_metrics: true
+use_gpu: true
+io:
+  require_complete_cache: false
+runtime:
+  executor: serial
+  fov_workers: 1
+  threads_per_worker: auto
+force_recompute:
+  final_metrics: true
+  pred_masks: true
+  pred_cp: true
+  pred_dinov3: true
+  pred_dynaclr: true
+  pred_celldino: true
+  pred_morphem: true
+  pred_instances: true
+conditions:
+- name: fnet3d_vscyto3daug_v2__ipsc_trained__a549_mock
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-sec61b-mock
+      target: sec61b
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/er/fnet3d_vscyto3daug_v2/ipsc/a549__mock/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/er/fnet3d_vscyto3daug_v2/ipsc/a549__mock
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/er/fnet3d_vscyto3daug_v2/ipsc/a549__mock
+- name: fnet3d_vscyto3daug_v2_seed1__ipsc_trained__a549_mock
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-sec61b-mock
+      target: sec61b
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/er/fnet3d_vscyto3daug_v2_seed1/ipsc/a549__mock/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/er/fnet3d_vscyto3daug_v2_seed1/ipsc/a549__mock
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/er/fnet3d_vscyto3daug_v2_seed1/ipsc/a549__mock

applications/dynacell/configs/benchmarks/virtual_staining/_internal/leaf/grouped/spotlight_v2_er_a549_mock__wave2t/eval_grouped.yaml

@@ -0,0 +1,35 @@
+# @package _global_
+# Spotlight-v2 bucket spotlight_v2_er_a549_mock__wave2t (1 conditions). Auto-generated by
+# tools/generate_spotlight_v2_eval_configs.py from spotlight_v2_eval_roster.yaml; edit the roster, not this file.
+# save_dir / pred_cache_dir live under /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2
+# (never the canonical dirs the paper reads); the GT caches are the shared manifest
+# ones. Every pred_* artifact is forced.
+target_name: er
+compute_feature_metrics: true
+use_gpu: true
+io:
+  require_complete_cache: false
+runtime:
+  executor: serial
+  fov_workers: 1
+  threads_per_worker: auto
+force_recompute:
+  final_metrics: true
+  pred_masks: true
+  pred_cp: true
+  pred_dinov3: true
+  pred_dynaclr: true
+  pred_celldino: true
+  pred_morphem: true
+  pred_instances: true
+conditions:
+- name: fnet3d_vscyto3daug_segaux__ipsc_trained__a549_mock
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-sec61b-mock
+      target: sec61b
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/er/fnet3d_vscyto3daug_segaux/ipsc/a549__mock/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/er/fnet3d_vscyto3daug_segaux/ipsc/a549__mock
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/er/fnet3d_vscyto3daug_segaux/ipsc/a549__mock

applications/dynacell/configs/benchmarks/virtual_staining/_internal/leaf/grouped/spotlight_v2_er_a549_mock__wave2x/eval_grouped.yaml

@@ -0,0 +1,35 @@
+# @package _global_
+# Spotlight-v2 bucket spotlight_v2_er_a549_mock__wave2x (1 conditions). Auto-generated by
+# tools/generate_spotlight_v2_eval_configs.py from spotlight_v2_eval_roster.yaml; edit the roster, not this file.
+# save_dir / pred_cache_dir live under /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2
+# (never the canonical dirs the paper reads); the GT caches are the shared manifest
+# ones. Every pred_* artifact is forced.
+target_name: er
+compute_feature_metrics: true
+use_gpu: true
+io:
+  require_complete_cache: false
+runtime:
+  executor: serial
+  fov_workers: 1
+  threads_per_worker: auto
+force_recompute:
+  final_metrics: true
+  pred_masks: true
+  pred_cp: true
+  pred_dinov3: true
+  pred_dynaclr: true
+  pred_celldino: true
+  pred_morphem: true
+  pred_instances: true
+conditions:
+- name: fnet3d_vscyto3daug_segaux_sauna__ipsc_trained__a549_mock
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-sec61b-mock
+      target: sec61b
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/er/fnet3d_vscyto3daug_segaux_sauna/ipsc/a549__mock/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/er/fnet3d_vscyto3daug_segaux_sauna/ipsc/a549__mock
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/er/fnet3d_vscyto3daug_segaux_sauna/ipsc/a549__mock

applications/dynacell/configs/benchmarks/virtual_staining/_internal/leaf/grouped/spotlight_v2_er_a549_mock__wave3b/eval_grouped.yaml

@@ -0,0 +1,35 @@
+# @package _global_
+# Spotlight-v2 bucket spotlight_v2_er_a549_mock__wave3b (1 conditions). Auto-generated by
+# tools/generate_spotlight_v2_eval_configs.py from spotlight_v2_eval_roster.yaml; edit the roster, not this file.
+# save_dir / pred_cache_dir live under /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2
+# (never the canonical dirs the paper reads); the GT caches are the shared manifest
+# ones. Every pred_* artifact is forced.
+target_name: er
+compute_feature_metrics: true
+use_gpu: true
+io:
+  require_complete_cache: false
+runtime:
+  executor: serial
+  fov_workers: 1
+  threads_per_worker: auto
+force_recompute:
+  final_metrics: true
+  pred_masks: true
+  pred_cp: true
+  pred_dinov3: true
+  pred_dynaclr: true
+  pred_celldino: true
+  pred_morphem: true
+  pred_instances: true
+conditions:
+- name: fnet3d_vscyto3daug_segaux_cldice__ipsc_trained__a549_mock
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-sec61b-mock
+      target: sec61b
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/er/fnet3d_vscyto3daug_segaux_cldice/ipsc/a549__mock/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/er/fnet3d_vscyto3daug_segaux_cldice/ipsc/a549__mock
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/er/fnet3d_vscyto3daug_segaux_cldice/ipsc/a549__mock

applications/dynacell/configs/benchmarks/virtual_staining/_internal/leaf/grouped/spotlight_v2_er_a549_mock__wave3h/eval_grouped.yaml

@@ -0,0 +1,35 @@
+# @package _global_
+# Spotlight-v2 bucket spotlight_v2_er_a549_mock__wave3h (1 conditions). Auto-generated by
+# tools/generate_spotlight_v2_eval_configs.py from spotlight_v2_eval_roster.yaml; edit the roster, not this file.
+# save_dir / pred_cache_dir live under /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2
+# (never the canonical dirs the paper reads); the GT caches are the shared manifest
+# ones. Every pred_* artifact is forced.
+target_name: er
+compute_feature_metrics: true
+use_gpu: true
+io:
+  require_complete_cache: false
+runtime:
+  executor: serial
+  fov_workers: 1
+  threads_per_worker: auto
+force_recompute:
+  final_metrics: true
+  pred_masks: true
+  pred_cp: true
+  pred_dinov3: true
+  pred_dynaclr: true
+  pred_celldino: true
+  pred_morphem: true
+  pred_instances: true
+conditions:
+- name: fnet3d_vscyto3daug_segaux_seed1__ipsc_trained__a549_mock
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-sec61b-mock
+      target: sec61b
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/er/fnet3d_vscyto3daug_segaux_seed1/ipsc/a549__mock/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/er/fnet3d_vscyto3daug_segaux_seed1/ipsc/a549__mock
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/er/fnet3d_vscyto3daug_segaux_seed1/ipsc/a549__mock