feat(dynacell): Spotlight v2 arm leaves, controls and eval waves

applications/dynacell/configs/benchmarks/virtual_staining/_internal/leaf/grouped/spotlight_v2_membrane_a549_denv__wave1c/eval_grouped.yaml

@@ -0,0 +1,40 @@
+# @package _global_
+# Spotlight-v2 bucket spotlight_v2_membrane_a549_denv__wave1c (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: membrane
+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
+compute_instance_ap: true
+segmentation:
+  backend: cpdino
+  nuclei_channel_name: Nuclei
+conditions:
+- name: pix2pix2d_last__ipsc_trained__a549_denv
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-caax-denv
+      target: caax
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/membrane/pix2pix2d_unetvit_last/ipsc/a549__denv/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/membrane/pix2pix2d_unetvit_last/ipsc/a549__denv
+    nuclei_gt_path: /hpc/projects/virtual_staining/training/dynacell/a549/mantis/test/dual_nucl_memb_DENV.zarr
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/membrane/pix2pix2d_unetvit_last/ipsc/a549__denv

applications/dynacell/configs/benchmarks/virtual_staining/_internal/leaf/grouped/spotlight_v2_membrane_a549_denv__wave1d/eval_grouped.yaml

@@ -0,0 +1,51 @@
+# @package _global_
+# Spotlight-v2 bucket spotlight_v2_membrane_a549_denv__wave1d (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: membrane
+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
+compute_instance_ap: true
+segmentation:
+  backend: cpdino
+  nuclei_channel_name: Nuclei
+conditions:
+- name: celldiff_2d_segaux__ipsc_trained__a549_denv
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-caax-denv
+      target: caax
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/membrane/celldiff_2d_segaux/ipsc/a549__denv/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/membrane/celldiff_2d_segaux/ipsc/a549__denv
+    nuclei_gt_path: /hpc/projects/virtual_staining/training/dynacell/a549/mantis/test/dual_nucl_memb_DENV.zarr
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/membrane/celldiff_2d_segaux/ipsc/a549__denv
+- name: unext2_2d_l1__ipsc_trained__a549_denv
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-caax-denv
+      target: caax
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/membrane/fcmae_vscyto2d_scratch_l1/ipsc/a549__denv/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/membrane/fcmae_vscyto2d_scratch_l1/ipsc/a549__denv
+    nuclei_gt_path: /hpc/projects/virtual_staining/training/dynacell/a549/mantis/test/dual_nucl_memb_DENV.zarr
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/membrane/fcmae_vscyto2d_scratch_l1/ipsc/a549__denv

applications/dynacell/configs/benchmarks/virtual_staining/_internal/leaf/grouped/spotlight_v2_membrane_a549_denv__wave2a/eval_grouped.yaml

@@ -0,0 +1,106 @@
+# @package _global_
+# Spotlight-v2 bucket spotlight_v2_membrane_a549_denv__wave2a (7 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: membrane
+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
+compute_instance_ap: true
+segmentation:
+  backend: cpdino
+  nuclei_channel_name: Nuclei
+conditions:
+- name: unext2_2d_l1segaux__ipsc_trained__a549_denv
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-caax-denv
+      target: caax
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/membrane/fcmae_vscyto2d_scratch_l1segaux/ipsc/a549__denv/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/membrane/fcmae_vscyto2d_scratch_l1segaux/ipsc/a549__denv
+    nuclei_gt_path: /hpc/projects/virtual_staining/training/dynacell/a549/mantis/test/dual_nucl_memb_DENV.zarr
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/membrane/fcmae_vscyto2d_scratch_l1segaux/ipsc/a549__denv
+- name: unext2_2d_segauxself__ipsc_trained__a549_denv
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-caax-denv
+      target: caax
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/membrane/fcmae_vscyto2d_scratch_segauxself/ipsc/a549__denv/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/membrane/fcmae_vscyto2d_scratch_segauxself/ipsc/a549__denv
+    nuclei_gt_path: /hpc/projects/virtual_staining/training/dynacell/a549/mantis/test/dual_nucl_memb_DENV.zarr
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/membrane/fcmae_vscyto2d_scratch_segauxself/ipsc/a549__denv
+- name: fnet2d_segauxself__ipsc_trained__a549_denv
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-caax-denv
+      target: caax
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/membrane/fnet2d_segauxself/ipsc/a549__denv/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/membrane/fnet2d_segauxself/ipsc/a549__denv
+    nuclei_gt_path: /hpc/projects/virtual_staining/training/dynacell/a549/mantis/test/dual_nucl_memb_DENV.zarr
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/membrane/fnet2d_segauxself/ipsc/a549__denv
+- name: fnet3d_segaux__ipsc_trained__a549_denv
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-caax-denv
+      target: caax
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/membrane/fnet3d_paper_segaux/ipsc/a549__denv/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/membrane/fnet3d_paper_segaux/ipsc/a549__denv
+    nuclei_gt_path: /hpc/projects/virtual_staining/training/dynacell/a549/mantis/test/dual_nucl_memb_DENV.zarr
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/membrane/fnet3d_paper_segaux/ipsc/a549__denv
+- name: pix2pix2d_segauxself__ipsc_trained__a549_denv
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-caax-denv
+      target: caax
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/membrane/pix2pix2d_unetvit_segauxself/ipsc/a549__denv/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/membrane/pix2pix2d_unetvit_segauxself/ipsc/a549__denv
+    nuclei_gt_path: /hpc/projects/virtual_staining/training/dynacell/a549/mantis/test/dual_nucl_memb_DENV.zarr
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/membrane/pix2pix2d_unetvit_segauxself/ipsc/a549__denv
+- name: pix2pix3d_segaux__ipsc_trained__a549_denv
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-caax-denv
+      target: caax
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/membrane/pix2pix3d_unetvit_segaux/ipsc/a549__denv/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/membrane/pix2pix3d_unetvit_segaux/ipsc/a549__denv
+    nuclei_gt_path: /hpc/projects/virtual_staining/training/dynacell/a549/mantis/test/dual_nucl_memb_DENV.zarr
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/membrane/pix2pix3d_unetvit_segaux/ipsc/a549__denv
+- name: pix2pix3d_v2__ipsc_trained__a549_denv
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-caax-denv
+      target: caax
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/membrane/pix2pix3d_unetvit_v2/ipsc/a549__denv/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/membrane/pix2pix3d_unetvit_v2/ipsc/a549__denv
+    nuclei_gt_path: /hpc/projects/virtual_staining/training/dynacell/a549/mantis/test/dual_nucl_memb_DENV.zarr
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/membrane/pix2pix3d_unetvit_v2/ipsc/a549__denv

applications/dynacell/configs/benchmarks/virtual_staining/_internal/leaf/grouped/spotlight_v2_membrane_a549_denv__wave2c/eval_grouped.yaml

@@ -0,0 +1,84 @@
+# @package _global_
+# Spotlight-v2 bucket spotlight_v2_membrane_a549_denv__wave2c (5 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: membrane
+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
+compute_instance_ap: true
+segmentation:
+  backend: cpdino
+  nuclei_channel_name: Nuclei
+conditions:
+- name: fnet2d_seed1__ipsc_trained__a549_denv
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-caax-denv
+      target: caax
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/membrane/fnet2d_seed1/ipsc/a549__denv/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/membrane/fnet2d_seed1/ipsc/a549__denv
+    nuclei_gt_path: /hpc/projects/virtual_staining/training/dynacell/a549/mantis/test/dual_nucl_memb_DENV.zarr
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/membrane/fnet2d_seed1/ipsc/a549__denv
+- name: unext2_2d_seed1__ipsc_trained__a549_denv
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-caax-denv
+      target: caax
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/membrane/fcmae_vscyto2d_scratch_seed1/ipsc/a549__denv/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/membrane/fcmae_vscyto2d_scratch_seed1/ipsc/a549__denv
+    nuclei_gt_path: /hpc/projects/virtual_staining/training/dynacell/a549/mantis/test/dual_nucl_memb_DENV.zarr
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/membrane/fcmae_vscyto2d_scratch_seed1/ipsc/a549__denv
+- name: pix2pix2d_seed1__ipsc_trained__a549_denv
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-caax-denv
+      target: caax
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/membrane/pix2pix2d_unetvit_seed1/ipsc/a549__denv/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/membrane/pix2pix2d_unetvit_seed1/ipsc/a549__denv
+    nuclei_gt_path: /hpc/projects/virtual_staining/training/dynacell/a549/mantis/test/dual_nucl_memb_DENV.zarr
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/membrane/pix2pix2d_unetvit_seed1/ipsc/a549__denv
+- name: unext2_2d_l1seed1__ipsc_trained__a549_denv
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-caax-denv
+      target: caax
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/membrane/fcmae_vscyto2d_scratch_l1seed1/ipsc/a549__denv/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/membrane/fcmae_vscyto2d_scratch_l1seed1/ipsc/a549__denv
+    nuclei_gt_path: /hpc/projects/virtual_staining/training/dynacell/a549/mantis/test/dual_nucl_memb_DENV.zarr
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/membrane/fcmae_vscyto2d_scratch_l1seed1/ipsc/a549__denv
+- name: unext2_v2__ipsc_trained__a549_denv
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-caax-denv
+      target: caax
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/membrane/fcmae_vscyto3d_scratch_v2/ipsc/a549__denv/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/membrane/fcmae_vscyto3d_scratch_v2/ipsc/a549__denv
+    nuclei_gt_path: /hpc/projects/virtual_staining/training/dynacell/a549/mantis/test/dual_nucl_memb_DENV.zarr
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/membrane/fcmae_vscyto3d_scratch_v2/ipsc/a549__denv

applications/dynacell/configs/benchmarks/virtual_staining/_internal/leaf/grouped/spotlight_v2_membrane_a549_denv__wave2f/eval_grouped.yaml

@@ -0,0 +1,51 @@
+# @package _global_
+# Spotlight-v2 bucket spotlight_v2_membrane_a549_denv__wave2f (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: membrane
+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
+compute_instance_ap: true
+segmentation:
+  backend: cpdino
+  nuclei_channel_name: Nuclei
+conditions:
+- name: fnet2d_segaux_seed1__ipsc_trained__a549_denv
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-caax-denv
+      target: caax
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/membrane/fnet2d_segaux_seed1/ipsc/a549__denv/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/membrane/fnet2d_segaux_seed1/ipsc/a549__denv
+    nuclei_gt_path: /hpc/projects/virtual_staining/training/dynacell/a549/mantis/test/dual_nucl_memb_DENV.zarr
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/membrane/fnet2d_segaux_seed1/ipsc/a549__denv
+- name: unext2_segaux__ipsc_trained__a549_denv
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-caax-denv
+      target: caax
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/membrane/fcmae_vscyto3d_scratch_segaux/ipsc/a549__denv/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/membrane/fcmae_vscyto3d_scratch_segaux/ipsc/a549__denv
+    nuclei_gt_path: /hpc/projects/virtual_staining/training/dynacell/a549/mantis/test/dual_nucl_memb_DENV.zarr
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/membrane/fcmae_vscyto3d_scratch_segaux/ipsc/a549__denv

applications/dynacell/configs/benchmarks/virtual_staining/_internal/leaf/grouped/spotlight_v2_membrane_a549_mock__wave1c/eval_grouped.yaml

@@ -0,0 +1,40 @@
+# @package _global_
+# Spotlight-v2 bucket spotlight_v2_membrane_a549_mock__wave1c (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: membrane
+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
+compute_instance_ap: true
+segmentation:
+  backend: cpdino
+  nuclei_channel_name: Nuclei
+conditions:
+- name: pix2pix2d_last__ipsc_trained__a549_mock
+  benchmark:
+    dataset_ref:
+      dataset: a549-mantis-caax-mock
+      target: caax
+  io:
+    pred_path: /hpc/projects/virtual_staining/training/dynacell/membrane/pix2pix2d_unetvit_last/ipsc/a549__mock/prediction.zarr
+    pred_cache_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/a549/eval_cache_pred/membrane/pix2pix2d_unetvit_last/ipsc/a549__mock
+    nuclei_gt_path: /hpc/projects/virtual_staining/training/dynacell/a549/mantis/test/dual_nucl_memb_mock.zarr
+  save:
+    save_dir: /hpc/projects/virtual_staining/training/dynacell/_spotlight_v2/membrane/pix2pix2d_unetvit_last/ipsc/a549__mock