feat(dynacell): pix2pix3d nucleus predict leaves wired to modernized GAN checkpoints

applications/dynacell/configs/benchmarks/virtual_staining/nucleus/pix2pix3d_unetvit/a549_mantis/predict__a549_mantis_denv.yml

@@ -0,0 +1,50 @@
+# pix2pix3d_unetvit predict: nucleus (Nuclei marker) trained on A549 mantis (h2b), predicting against a549_mantis_h2b_denv test.
+base:
+  - ../../../_internal/shared/model/predict_sets/a549_mantis_h2b_denv.yml
+  - ../../../_internal/shared/model/targets/nucleus.yml
+  - ../../../_internal/shared/model/model_overlays/pix2pix3d_unetvit_predict.yml
+  - ../../../_internal/shared/model/launcher_profiles/mode_predict.yml
+  - ../../../_internal/shared/model/launcher_profiles/hardware_predict_any_gpu.yml
+  - ../../../_internal/shared/model/launcher_profiles/runtime_shared.yml
+
+benchmark:
+  task: virtual_staining
+  organelle: nucleus
+  trained_on: a549_mantis
+  predict_set: a549_mantis_h2b_denv
+  model_name: pix2pix3d_unetvit
+  experiment_id: nucleus__a549_mantis__pix2pix3d_unetvit__a549_mantis_h2b_denv
+  # A549 manifest keys nucleus by gene (`h2b`); override the iPSC-side
+  # `nucleus` target from targets/nucleus.yml so the resolver finds h2b.
+  dataset_ref:
+    target: h2b
+
+model:
+  init_args:
+    # Best loss/validate_ema checkpoint, modernized Run-D 40ep run (job
+    # 33501550, best at epoch 39, validate_ema=1.51563). predict_step uses
+    # generator_ema (use_ema_at_predict=True default).
+    ckpt_path: /hpc/projects/comp.micro/virtual_staining/models/cell_diff_vs_viscy/a549_mantis/nucl/pix2pix3d_unetvit_modernized_lambdaL1_10_lecam_40ep/checkpoints/epoch=39-step=86400.ckpt
+
+data:
+  init_args:
+    # override target-inherited normalizations: predict only reads source
+    normalizations:
+      - class_path: viscy_transforms.NormalizeSampled
+        init_args:
+          keys: [Phase3D]
+          level: fov_statistics
+          subtrahend: mean
+          divisor: std
+    # clear target-inherited RandWeightedCropd; predict has no CPU augs
+    augmentations: []
+
+trainer:
+  callbacks:
+    - class_path: viscy_utils.callbacks.prediction_writer.HCSPredictionWriter
+      init_args:
+        output_store: /hpc/projects/virtual_staining/training/dynacell/a549/predictions/nucl_pix2pix3d_unetvit_a549trained__h2b_denv.zarr
+
+launcher:
+  job_name: pix2pix3d_unetvit_A549TR_PRED_NUCL_h2b_denv
+  run_root: /hpc/projects/virtual_staining/training/dynacell/a549/predictions

applications/dynacell/configs/benchmarks/virtual_staining/nucleus/pix2pix3d_unetvit/a549_mantis/predict__a549_mantis_mock.yml

@@ -0,0 +1,50 @@
+# pix2pix3d_unetvit predict: nucleus (Nuclei marker) trained on A549 mantis (h2b), predicting against a549_mantis_h2b_mock test.
+base:
+  - ../../../_internal/shared/model/predict_sets/a549_mantis_h2b_mock.yml
+  - ../../../_internal/shared/model/targets/nucleus.yml
+  - ../../../_internal/shared/model/model_overlays/pix2pix3d_unetvit_predict.yml
+  - ../../../_internal/shared/model/launcher_profiles/mode_predict.yml
+  - ../../../_internal/shared/model/launcher_profiles/hardware_predict_any_gpu.yml
+  - ../../../_internal/shared/model/launcher_profiles/runtime_shared.yml
+
+benchmark:
+  task: virtual_staining
+  organelle: nucleus
+  trained_on: a549_mantis
+  predict_set: a549_mantis_h2b_mock
+  model_name: pix2pix3d_unetvit
+  experiment_id: nucleus__a549_mantis__pix2pix3d_unetvit__a549_mantis_h2b_mock
+  # A549 manifest keys nucleus by gene (`h2b`); override the iPSC-side
+  # `nucleus` target from targets/nucleus.yml so the resolver finds h2b.
+  dataset_ref:
+    target: h2b
+
+model:
+  init_args:
+    # Best loss/validate_ema checkpoint, modernized Run-D 40ep run (job
+    # 33501550, best at epoch 39, validate_ema=1.51563). predict_step uses
+    # generator_ema (use_ema_at_predict=True default).
+    ckpt_path: /hpc/projects/comp.micro/virtual_staining/models/cell_diff_vs_viscy/a549_mantis/nucl/pix2pix3d_unetvit_modernized_lambdaL1_10_lecam_40ep/checkpoints/epoch=39-step=86400.ckpt
+
+data:
+  init_args:
+    # override target-inherited normalizations: predict only reads source
+    normalizations:
+      - class_path: viscy_transforms.NormalizeSampled
+        init_args:
+          keys: [Phase3D]
+          level: fov_statistics
+          subtrahend: mean
+          divisor: std
+    # clear target-inherited RandWeightedCropd; predict has no CPU augs
+    augmentations: []
+
+trainer:
+  callbacks:
+    - class_path: viscy_utils.callbacks.prediction_writer.HCSPredictionWriter
+      init_args:
+        output_store: /hpc/projects/virtual_staining/training/dynacell/a549/predictions/nucl_pix2pix3d_unetvit_a549trained__h2b_mock.zarr
+
+launcher:
+  job_name: pix2pix3d_unetvit_A549TR_PRED_NUCL_h2b_mock
+  run_root: /hpc/projects/virtual_staining/training/dynacell/a549/predictions

applications/dynacell/configs/benchmarks/virtual_staining/nucleus/pix2pix3d_unetvit/a549_mantis/predict__a549_mantis_zikv.yml

@@ -0,0 +1,50 @@
+# pix2pix3d_unetvit predict: nucleus (Nuclei marker) trained on A549 mantis (h2b), predicting against a549_mantis_h2b_zikv test.
+base:
+  - ../../../_internal/shared/model/predict_sets/a549_mantis_h2b_zikv.yml
+  - ../../../_internal/shared/model/targets/nucleus.yml
+  - ../../../_internal/shared/model/model_overlays/pix2pix3d_unetvit_predict.yml
+  - ../../../_internal/shared/model/launcher_profiles/mode_predict.yml
+  - ../../../_internal/shared/model/launcher_profiles/hardware_predict_any_gpu.yml
+  - ../../../_internal/shared/model/launcher_profiles/runtime_shared.yml
+
+benchmark:
+  task: virtual_staining
+  organelle: nucleus
+  trained_on: a549_mantis
+  predict_set: a549_mantis_h2b_zikv
+  model_name: pix2pix3d_unetvit
+  experiment_id: nucleus__a549_mantis__pix2pix3d_unetvit__a549_mantis_h2b_zikv
+  # A549 manifest keys nucleus by gene (`h2b`); override the iPSC-side
+  # `nucleus` target from targets/nucleus.yml so the resolver finds h2b.
+  dataset_ref:
+    target: h2b
+
+model:
+  init_args:
+    # Best loss/validate_ema checkpoint, modernized Run-D 40ep run (job
+    # 33501550, best at epoch 39, validate_ema=1.51563). predict_step uses
+    # generator_ema (use_ema_at_predict=True default).
+    ckpt_path: /hpc/projects/comp.micro/virtual_staining/models/cell_diff_vs_viscy/a549_mantis/nucl/pix2pix3d_unetvit_modernized_lambdaL1_10_lecam_40ep/checkpoints/epoch=39-step=86400.ckpt
+
+data:
+  init_args:
+    # override target-inherited normalizations: predict only reads source
+    normalizations:
+      - class_path: viscy_transforms.NormalizeSampled
+        init_args:
+          keys: [Phase3D]
+          level: fov_statistics
+          subtrahend: mean
+          divisor: std
+    # clear target-inherited RandWeightedCropd; predict has no CPU augs
+    augmentations: []
+
+trainer:
+  callbacks:
+    - class_path: viscy_utils.callbacks.prediction_writer.HCSPredictionWriter
+      init_args:
+        output_store: /hpc/projects/virtual_staining/training/dynacell/a549/predictions/nucl_pix2pix3d_unetvit_a549trained__h2b_zikv.zarr
+
+launcher:
+  job_name: pix2pix3d_unetvit_A549TR_PRED_NUCL_h2b_zikv
+  run_root: /hpc/projects/virtual_staining/training/dynacell/a549/predictions

applications/dynacell/configs/benchmarks/virtual_staining/nucleus/pix2pix3d_unetvit/a549_mantis/predict__ipsc_confocal.yml

@@ -0,0 +1,46 @@
+# pix2pix3d_unetvit predict: nucleus (Nuclei marker) trained on A549 mantis (h2b), predicting against ipsc_confocal test_cropped.
+base:
+  - ../../../_internal/shared/model/predict_sets/ipsc_confocal.yml
+  - ../../../_internal/shared/model/targets/nucleus.yml
+  - ../../../_internal/shared/model/model_overlays/pix2pix3d_unetvit_predict.yml
+  - ../../../_internal/shared/model/launcher_profiles/mode_predict.yml
+  - ../../../_internal/shared/model/launcher_profiles/hardware_predict_any_gpu.yml
+  - ../../../_internal/shared/model/launcher_profiles/runtime_shared.yml
+
+benchmark:
+  task: virtual_staining
+  organelle: nucleus
+  trained_on: a549_mantis
+  predict_set: ipsc_confocal
+  model_name: pix2pix3d_unetvit
+  experiment_id: nucleus__a549_mantis__pix2pix3d_unetvit__ipsc_confocal
+
+model:
+  init_args:
+    # Best loss/validate_ema checkpoint, modernized Run-D 40ep run (job
+    # 33501550, best at epoch 39, validate_ema=1.51563). predict_step uses
+    # generator_ema (use_ema_at_predict=True default).
+    ckpt_path: /hpc/projects/comp.micro/virtual_staining/models/cell_diff_vs_viscy/a549_mantis/nucl/pix2pix3d_unetvit_modernized_lambdaL1_10_lecam_40ep/checkpoints/epoch=39-step=86400.ckpt
+
+data:
+  init_args:
+    # override target-inherited normalizations: predict only reads source
+    normalizations:
+      - class_path: viscy_transforms.NormalizeSampled
+        init_args:
+          keys: [Phase3D]
+          level: fov_statistics
+          subtrahend: mean
+          divisor: std
+    # clear target-inherited RandWeightedCropd; predict has no CPU augs
+    augmentations: []
+
+trainer:
+  callbacks:
+    - class_path: viscy_utils.callbacks.prediction_writer.HCSPredictionWriter
+      init_args:
+        output_store: /hpc/projects/virtual_staining/training/dynacell/ipsc/predictions/nucl_pix2pix3d_unetvit_a549trained.zarr
+
+launcher:
+  job_name: pix2pix3d_unetvit_A549TR_PRED_NUCL_ON_IPSC
+  run_root: /hpc/projects/virtual_staining/training/dynacell/ipsc/predictions

applications/dynacell/configs/benchmarks/virtual_staining/nucleus/pix2pix3d_unetvit/ipsc_confocal/predict__a549_mantis_denv.yml

@@ -14,10 +14,17 @@ benchmark:
   predict_set: a549_mantis_h2b_denv
   model_name: pix2pix3d_unetvit
   experiment_id: nucleus__ipsc_confocal__pix2pix3d_unetvit__a549_mantis_h2b_denv
+  # A549 manifest keys nucleus by gene (`h2b`); override the iPSC-side
+  # `nucleus` target from targets/nucleus.yml so the resolver finds h2b.
+  dataset_ref:
+    target: h2b
 
 model:
   init_args:
-    ckpt_path: REPLACE_ME_WITH_PRODUCTION_CHECKPOINT_PATH
+    # Best loss/validate_ema checkpoint, modernized Run-D 40ep run (job
+    # 33501549, converged early at epoch 15). predict_step uses generator_ema
+    # (use_ema_at_predict=True default).
+    ckpt_path: /hpc/projects/comp.micro/virtual_staining/models/cell_diff_vs_viscy/ipsc/nucl/pix2pix3d_unetvit_modernized_lambdaL1_10_lecam_40ep/checkpoints/epoch=15-step=51200.ckpt
 
 data:
   init_args:

applications/dynacell/configs/benchmarks/virtual_staining/nucleus/pix2pix3d_unetvit/ipsc_confocal/predict__a549_mantis_mock.yml

@@ -14,10 +14,17 @@ benchmark:
   predict_set: a549_mantis_h2b_mock
   model_name: pix2pix3d_unetvit
   experiment_id: nucleus__ipsc_confocal__pix2pix3d_unetvit__a549_mantis_h2b_mock
+  # A549 manifest keys nucleus by gene (`h2b`); override the iPSC-side
+  # `nucleus` target from targets/nucleus.yml so the resolver finds h2b.
+  dataset_ref:
+    target: h2b
 
 model:
   init_args:
-    ckpt_path: REPLACE_ME_WITH_PRODUCTION_CHECKPOINT_PATH
+    # Best loss/validate_ema checkpoint, modernized Run-D 40ep run (job
+    # 33501549, converged early at epoch 15). predict_step uses generator_ema
+    # (use_ema_at_predict=True default).
+    ckpt_path: /hpc/projects/comp.micro/virtual_staining/models/cell_diff_vs_viscy/ipsc/nucl/pix2pix3d_unetvit_modernized_lambdaL1_10_lecam_40ep/checkpoints/epoch=15-step=51200.ckpt
 
 data:
   init_args:

applications/dynacell/configs/benchmarks/virtual_staining/nucleus/pix2pix3d_unetvit/ipsc_confocal/predict__a549_mantis_zikv.yml

@@ -14,10 +14,17 @@ benchmark:
   predict_set: a549_mantis_h2b_zikv
   model_name: pix2pix3d_unetvit
   experiment_id: nucleus__ipsc_confocal__pix2pix3d_unetvit__a549_mantis_h2b_zikv
+  # A549 manifest keys nucleus by gene (`h2b`); override the iPSC-side
+  # `nucleus` target from targets/nucleus.yml so the resolver finds h2b.
+  dataset_ref:
+    target: h2b
 
 model:
   init_args:
-    ckpt_path: REPLACE_ME_WITH_PRODUCTION_CHECKPOINT_PATH
+    # Best loss/validate_ema checkpoint, modernized Run-D 40ep run (job
+    # 33501549, converged early at epoch 15). predict_step uses generator_ema
+    # (use_ema_at_predict=True default).
+    ckpt_path: /hpc/projects/comp.micro/virtual_staining/models/cell_diff_vs_viscy/ipsc/nucl/pix2pix3d_unetvit_modernized_lambdaL1_10_lecam_40ep/checkpoints/epoch=15-step=51200.ckpt
 
 data:
   init_args:

applications/dynacell/configs/benchmarks/virtual_staining/nucleus/pix2pix3d_unetvit/ipsc_confocal/predict__ipsc_confocal.yml

@@ -17,7 +17,10 @@ benchmark:
 
 model:
   init_args:
-    ckpt_path: REPLACE_ME_WITH_PRODUCTION_CHECKPOINT_PATH
+    # Best loss/validate_ema checkpoint, modernized Run-D 40ep run (job
+    # 33501549, converged early at epoch 15). predict_step uses generator_ema
+    # (use_ema_at_predict=True default).
+    ckpt_path: /hpc/projects/comp.micro/virtual_staining/models/cell_diff_vs_viscy/ipsc/nucl/pix2pix3d_unetvit_modernized_lambdaL1_10_lecam_40ep/checkpoints/epoch=15-step=51200.ckpt
 
 data:
   init_args:

applications/dynacell/configs/benchmarks/virtual_staining/nucleus/pix2pix3d_unetvit/joint_ipsc_confocal_a549_mantis/predict__a549_mantis_denv.yml

@@ -14,10 +14,17 @@ benchmark:
   predict_set: a549_mantis_h2b_denv
   model_name: pix2pix3d_unetvit
   experiment_id: nucleus__joint_ipsc_confocal_a549_mantis__pix2pix3d_unetvit__a549_mantis_h2b_denv
+  # A549 manifest keys nucleus by gene (`h2b`); override the iPSC-side
+  # `nucleus` target from targets/nucleus.yml so the resolver finds h2b.
+  dataset_ref:
+    target: h2b
 
 model:
   init_args:
-    ckpt_path: /hpc/projects/comp.micro/virtual_staining/models/dynacell/joint_ipsc_confocal_a549_mantis/nucl/pix2pix3d_unetvit/checkpoints/last.ckpt
+    # Best loss/validate_ema checkpoint, modernized Run-D 40ep run (job
+    # 33502019, best at epoch 39, validate_ema=1.00041). predict_step uses
+    # generator_ema (use_ema_at_predict=True default).
+    ckpt_path: /hpc/projects/comp.micro/virtual_staining/models/cell_diff_vs_viscy/joint_ipsc_confocal_a549_mantis/nucl/pix2pix3d_unetvit_modernized_lambdaL1_10_lecam_40ep/checkpoints/epoch=39-step=214400.ckpt
 
 data:
   init_args:

applications/dynacell/configs/benchmarks/virtual_staining/nucleus/pix2pix3d_unetvit/joint_ipsc_confocal_a549_mantis/predict__a549_mantis_mock.yml

@@ -14,10 +14,17 @@ benchmark:
   predict_set: a549_mantis_h2b_mock
   model_name: pix2pix3d_unetvit
   experiment_id: nucleus__joint_ipsc_confocal_a549_mantis__pix2pix3d_unetvit__a549_mantis_h2b_mock
+  # A549 manifest keys nucleus by gene (`h2b`); override the iPSC-side
+  # `nucleus` target from targets/nucleus.yml so the resolver finds h2b.
+  dataset_ref:
+    target: h2b
 
 model:
   init_args:
-    ckpt_path: /hpc/projects/comp.micro/virtual_staining/models/dynacell/joint_ipsc_confocal_a549_mantis/nucl/pix2pix3d_unetvit/checkpoints/last.ckpt
+    # Best loss/validate_ema checkpoint, modernized Run-D 40ep run (job
+    # 33502019, best at epoch 39, validate_ema=1.00041). predict_step uses
+    # generator_ema (use_ema_at_predict=True default).
+    ckpt_path: /hpc/projects/comp.micro/virtual_staining/models/cell_diff_vs_viscy/joint_ipsc_confocal_a549_mantis/nucl/pix2pix3d_unetvit_modernized_lambdaL1_10_lecam_40ep/checkpoints/epoch=39-step=214400.ckpt
 
 data:
   init_args:

applications/dynacell/configs/benchmarks/virtual_staining/nucleus/pix2pix3d_unetvit/joint_ipsc_confocal_a549_mantis/predict__a549_mantis_zikv.yml

@@ -14,10 +14,17 @@ benchmark:
   predict_set: a549_mantis_h2b_zikv
   model_name: pix2pix3d_unetvit
   experiment_id: nucleus__joint_ipsc_confocal_a549_mantis__pix2pix3d_unetvit__a549_mantis_h2b_zikv
+  # A549 manifest keys nucleus by gene (`h2b`); override the iPSC-side
+  # `nucleus` target from targets/nucleus.yml so the resolver finds h2b.
+  dataset_ref:
+    target: h2b
 
 model:
   init_args:
-    ckpt_path: /hpc/projects/comp.micro/virtual_staining/models/dynacell/joint_ipsc_confocal_a549_mantis/nucl/pix2pix3d_unetvit/checkpoints/last.ckpt
+    # Best loss/validate_ema checkpoint, modernized Run-D 40ep run (job
+    # 33502019, best at epoch 39, validate_ema=1.00041). predict_step uses
+    # generator_ema (use_ema_at_predict=True default).
+    ckpt_path: /hpc/projects/comp.micro/virtual_staining/models/cell_diff_vs_viscy/joint_ipsc_confocal_a549_mantis/nucl/pix2pix3d_unetvit_modernized_lambdaL1_10_lecam_40ep/checkpoints/epoch=39-step=214400.ckpt
 
 data:
   init_args:

applications/dynacell/configs/benchmarks/virtual_staining/nucleus/pix2pix3d_unetvit/joint_ipsc_confocal_a549_mantis/predict__ipsc_confocal.yml

@@ -17,7 +17,10 @@ benchmark:
 
 model:
   init_args:
-    ckpt_path: /hpc/projects/comp.micro/virtual_staining/models/dynacell/joint_ipsc_confocal_a549_mantis/nucl/pix2pix3d_unetvit/checkpoints/last.ckpt
+    # Best loss/validate_ema checkpoint, modernized Run-D 40ep run (job
+    # 33502019, best at epoch 39, validate_ema=1.00041). predict_step uses
+    # generator_ema (use_ema_at_predict=True default).
+    ckpt_path: /hpc/projects/comp.micro/virtual_staining/models/cell_diff_vs_viscy/joint_ipsc_confocal_a549_mantis/nucl/pix2pix3d_unetvit_modernized_lambdaL1_10_lecam_40ep/checkpoints/epoch=39-step=214400.ckpt
 
 data:
   init_args: