update and add split files

NASH_steato/README.md

@@ -9,13 +9,10 @@ Static2Dynamic pretrained checkpoint.
 - `video_time_encoder/config.json`
 - `video_time_encoder/diffusion_pytorch_model.safetensors`
 - `dynamic/scheduler_config.json`
-- `training_state_info.json`, when available
 - `my_conf/`, when available
-
-## Provenance
-
-- Local run folder: `NASH_steato_JZ_download`
-- Local checkpoint subfolder: `saved_model`
+- `train_samples.parquet`, when available
+- `test_samples.parquet`, when available
+- `training_state_info.json`, when available
 
 ## Download
 

NASH_steato/source.txt

@@ -1,3 +0,0 @@
-local_run: NASH_steato_JZ_download
-checkpoint_subdir: saved_model
-hf_checkpoint_name: NASH_steato

README.md

@@ -16,33 +16,33 @@ pipeline_tag: image-to-video
 
 Pretrained checkpoints for **Static2Dynamic**, a method for reconstructing videos of unobservable cellular, developmental, and disease processes from static, unpaired snapshots.
 
-Code repository: `https://github.com/biocompibens/static2dynamic`
-
-Paper/preprint: `https://www.biorxiv.org/content/10.64898/2026.05.18.725860v1`
+- [Code repository](https://github.com/biocompibens/static2dynamic)
+- [Paper/preprint](https://www.biorxiv.org/content/10.64898/2026.05.18.725860)
 
 ## Checkpoints
 
 Each checkpoint subfolder contains:
 
-- `net/`: diffusion generative model config and weights
-- `video_time_encoder/`: time conditioning encoder config and weights
+- `net/`: diffusion/image generative model config and weights
+- `video_time_encoder/`: time/video conditioning encoder config and weights
 - `dynamic/`: scheduler configuration
 - `my_conf/`: run configuration needed to instantiate/evaluate the model
+- `train_samples.parquet`: training split metadata, when available
+- `test_samples.parquet`: test split metadata, when available
 - `training_state_info.json`: checkpoint/training metadata, when available
-- `source.txt`: local provenance marker for this release
-
-| Checkpoint | Local source run | Local checkpoint |
-|---|---|---|
-| `chromalive` | `chromalive_high_doses` | `best_model` |
-| `docetaxel_skip_half_doses` | `bbbc021_docetaxel_skip_half_doses` | `best_model` |
-| `docetaxel` | `bbbc021_JZ_download` | `saved_model` |
-| `nocodazole` | `bbbc021_nocodazole_no_xattn_no_reweight` | `best_model` |
-| `cell_cycle` | `bbbc048` | `best_model` |
-| `biotine` | `biotine_png_JZ_download` | `saved_model` |
-| `biotine_unpaired` | `biotine_unpaired` | `best_model` |
-| `ependymal` | `ependymal_cutout_noised0.1_fc_augs` | `last_model` |
-| `NASH_steato` | `NASH_steato_JZ_download` | `saved_model` |
-| `diabetic_retinopathy` | `retino_fc_precrop_2048_noreweight_6M` | `best_model` |
+
+| Checkpoint | Files |
+|---|---|
+| [`chromalive`](./chromalive) | `net/`, `video_time_encoder/`, `dynamic/`, `my_conf/`, `train_samples.parquet`, `test_samples.parquet`, `training_state_info.json` |
+| [`docetaxel_skip_half_doses`](./docetaxel_skip_half_doses) | `net/`, `video_time_encoder/`, `dynamic/`, `my_conf/`, `train_samples.parquet`, `test_samples.parquet`, `training_state_info.json` |
+| [`docetaxel`](./docetaxel) | `net/`, `video_time_encoder/`, `dynamic/`, `my_conf/`, `training_state_info.json` |
+| [`nocodazole`](./nocodazole) | `net/`, `video_time_encoder/`, `dynamic/`, `my_conf/`, `test_samples.parquet`, `training_state_info.json` |
+| [`cell_cycle`](./cell_cycle) | `net/`, `video_time_encoder/`, `dynamic/`, `my_conf/`, `train_samples.parquet`, `test_samples.parquet`, `training_state_info.json` |
+| [`biotine`](./biotine) | `net/`, `video_time_encoder/`, `dynamic/`, `my_conf/`, `training_state_info.json` |
+| [`biotine_unpaired`](./biotine_unpaired) | `net/`, `video_time_encoder/`, `dynamic/`, `my_conf/`, `train_samples.parquet`, `test_samples.parquet`, `training_state_info.json` |
+| [`ependymal`](./ependymal) | `net/`, `video_time_encoder/`, `dynamic/`, `my_conf/`, `train_samples.parquet`, `test_samples.parquet`, `training_state_info.json` |
+| [`NASH_steato`](./NASH_steato) | `net/`, `video_time_encoder/`, `dynamic/`, `my_conf/`, `training_state_info.json` |
+| [`diabetic_retinopathy`](./diabetic_retinopathy) | `net/`, `video_time_encoder/`, `dynamic/`, `my_conf/`, `train_samples.parquet`, `test_samples.parquet`, `training_state_info.json` |
 
 ## Python download example
 

biotine/README.md

@@ -9,13 +9,10 @@ Static2Dynamic pretrained checkpoint.
 - `video_time_encoder/config.json`
 - `video_time_encoder/diffusion_pytorch_model.safetensors`
 - `dynamic/scheduler_config.json`
-- `training_state_info.json`, when available
 - `my_conf/`, when available
-
-## Provenance
-
-- Local run folder: `biotine_png_JZ_download`
-- Local checkpoint subfolder: `saved_model`
+- `train_samples.parquet`, when available
+- `test_samples.parquet`, when available
+- `training_state_info.json`, when available
 
 ## Download
 

biotine/source.txt

@@ -1,3 +0,0 @@
-local_run: biotine_png_JZ_download
-checkpoint_subdir: saved_model
-hf_checkpoint_name: biotine

biotine_unpaired/README.md

@@ -9,13 +9,10 @@ Static2Dynamic pretrained checkpoint.
 - `video_time_encoder/config.json`
 - `video_time_encoder/diffusion_pytorch_model.safetensors`
 - `dynamic/scheduler_config.json`
-- `training_state_info.json`, when available
 - `my_conf/`, when available
-
-## Provenance
-
-- Local run folder: `biotine_unpaired`
-- Local checkpoint subfolder: `best_model`
+- `train_samples.parquet`, when available
+- `test_samples.parquet`, when available
+- `training_state_info.json`, when available
 
 ## Download
 

biotine_unpaired/source.txt

@@ -1,3 +0,0 @@
-local_run: biotine_unpaired
-checkpoint_subdir: best_model
-hf_checkpoint_name: biotine_unpaired

biotine_unpaired/test_samples.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:7482833b8a4c5d0190fd30d20884109e4183f4a68c50ae4ad44b2fd12cf926aa
+size 546832

biotine_unpaired/train_samples.parquet

@@ -0,0 +1,3 @@
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+oid sha256:fec8b57408745647d84d725fb224294cec2ae673dbdfc4117937e3de61612e90
+size 151272

cell_cycle/README.md

@@ -9,13 +9,10 @@ Static2Dynamic pretrained checkpoint.
 - `video_time_encoder/config.json`
 - `video_time_encoder/diffusion_pytorch_model.safetensors`
 - `dynamic/scheduler_config.json`
-- `training_state_info.json`, when available
 - `my_conf/`, when available
-
-## Provenance
-
-- Local run folder: `bbbc048`
-- Local checkpoint subfolder: `best_model`
+- `train_samples.parquet`, when available
+- `test_samples.parquet`, when available
+- `training_state_info.json`, when available
 
 ## Download
 

cell_cycle/source.txt

@@ -1,3 +0,0 @@
-local_run: bbbc048
-checkpoint_subdir: best_model
-hf_checkpoint_name: cell_cycle

cell_cycle/test_samples.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:085ab3419d1e5e55bac5f3b23efc3188c46025805713be8dec31b0f6f99cac6f
+size 144701

cell_cycle/train_samples.parquet

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+oid sha256:03c7d02cbfef701f83e54eca528228d291ad3ee034c118a1d6417116003a7be8
+size 959641

chromalive/README.md

@@ -9,13 +9,10 @@ Static2Dynamic pretrained checkpoint.
 - `video_time_encoder/config.json`
 - `video_time_encoder/diffusion_pytorch_model.safetensors`
 - `dynamic/scheduler_config.json`
-- `training_state_info.json`, when available
 - `my_conf/`, when available
-
-## Provenance
-
-- Local run folder: `chromalive_high_doses`
-- Local checkpoint subfolder: `best_model`
+- `train_samples.parquet`, when available
+- `test_samples.parquet`, when available
+- `training_state_info.json`, when available
 
 ## Download
 

chromalive/source.txt

@@ -1,3 +0,0 @@
-local_run: chromalive_high_doses
-checkpoint_subdir: best_model
-hf_checkpoint_name: chromalive

chromalive/test_samples.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:3f97d9a4df112aa396d54398cccb32d4386bd1d97ab17a9f949fa28ba0d06d4e
+size 1843785

chromalive/train_samples.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:46139e3429db4054d17aed39f0d260f42af742f5aca0cd7937cabf047f915815
+size 14902715

diabetic_retinopathy/README.md

@@ -9,13 +9,10 @@ Static2Dynamic pretrained checkpoint.
 - `video_time_encoder/config.json`
 - `video_time_encoder/diffusion_pytorch_model.safetensors`
 - `dynamic/scheduler_config.json`
-- `training_state_info.json`, when available
 - `my_conf/`, when available
-
-## Provenance
-
-- Local run folder: `retino_fc_precrop_2048_noreweight_6M`
-- Local checkpoint subfolder: `best_model`
+- `train_samples.parquet`, when available
+- `test_samples.parquet`, when available
+- `training_state_info.json`, when available
 
 ## Download
 

diabetic_retinopathy/source.txt

@@ -1,3 +0,0 @@
-local_run: retino_fc_precrop_2048_noreweight_6M
-checkpoint_subdir: best_model
-hf_checkpoint_name: diabetic_retinopathy

diabetic_retinopathy/test_samples.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:fe563781886cff20c97642a5c575cdd8887171408bb6e9742352dd9c0e587f1e
+size 445874

diabetic_retinopathy/train_samples.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a60308bc3e20db64985bf9c5e1dc48c20357848eba4eb44fdfde0dfca3f8378f
+size 2935868

docetaxel/README.md

@@ -9,13 +9,10 @@ Static2Dynamic pretrained checkpoint.
 - `video_time_encoder/config.json`
 - `video_time_encoder/diffusion_pytorch_model.safetensors`
 - `dynamic/scheduler_config.json`
-- `training_state_info.json`, when available
 - `my_conf/`, when available
-
-## Provenance
-
-- Local run folder: `bbbc021_JZ_download`
-- Local checkpoint subfolder: `saved_model`
+- `train_samples.parquet`, when available
+- `test_samples.parquet`, when available
+- `training_state_info.json`, when available
 
 ## Download
 

docetaxel/source.txt

@@ -1,3 +0,0 @@
-local_run: bbbc021_JZ_download
-checkpoint_subdir: saved_model
-hf_checkpoint_name: docetaxel

docetaxel_skip_half_doses/README.md

@@ -9,13 +9,10 @@ Static2Dynamic pretrained checkpoint.
 - `video_time_encoder/config.json`
 - `video_time_encoder/diffusion_pytorch_model.safetensors`
 - `dynamic/scheduler_config.json`
-- `training_state_info.json`, when available
 - `my_conf/`, when available
-
-## Provenance
-
-- Local run folder: `bbbc021_docetaxel_skip_half_doses`
-- Local checkpoint subfolder: `best_model`
+- `train_samples.parquet`, when available
+- `test_samples.parquet`, when available
+- `training_state_info.json`, when available
 
 ## Download
 

docetaxel_skip_half_doses/source.txt

@@ -1,3 +0,0 @@
-local_run: bbbc021_docetaxel_skip_half_doses
-checkpoint_subdir: best_model
-hf_checkpoint_name: docetaxel_skip_half_doses

docetaxel_skip_half_doses/test_samples.parquet

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+oid sha256:c0f489e2aa811ef316e2aa68822f5873d3d472a30d99e7252e9d7c1e6f372ca1
+size 10410

docetaxel_skip_half_doses/train_samples.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:83edc96bb7736260a93396431674c3e1dbdaf27aa40e36a679852e117dde5877
+size 59574

ependymal/README.md

@@ -9,13 +9,10 @@ Static2Dynamic pretrained checkpoint.
 - `video_time_encoder/config.json`
 - `video_time_encoder/diffusion_pytorch_model.safetensors`
 - `dynamic/scheduler_config.json`
-- `training_state_info.json`, when available
 - `my_conf/`, when available
-
-## Provenance
-
-- Local run folder: `ependymal_cutout_noised0.1_fc_augs`
-- Local checkpoint subfolder: `last_model`
+- `train_samples.parquet`, when available
+- `test_samples.parquet`, when available
+- `training_state_info.json`, when available
 
 ## Download
 

ependymal/source.txt

@@ -1,3 +0,0 @@
-local_run: ependymal_cutout_noised0.1_fc_augs
-checkpoint_subdir: last_model
-hf_checkpoint_name: ependymal

ependymal/test_samples.parquet

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+size 2438504

ependymal/train_samples.parquet

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+version https://git-lfs.github.com/spec/v1
+oid sha256:24d669410862adfc8588ed63d4c8107174c597ddbbfc443b43ef9dbd0f5288c1
+size 23034793

nocodazole/README.md

@@ -9,13 +9,10 @@ Static2Dynamic pretrained checkpoint.
 - `video_time_encoder/config.json`
 - `video_time_encoder/diffusion_pytorch_model.safetensors`
 - `dynamic/scheduler_config.json`
-- `training_state_info.json`, when available
 - `my_conf/`, when available
-
-## Provenance
-
-- Local run folder: `bbbc021_nocodazole_no_xattn_no_reweight`
-- Local checkpoint subfolder: `best_model`
+- `train_samples.parquet`, when available
+- `test_samples.parquet`, when available
+- `training_state_info.json`, when available
 
 ## Download
 

nocodazole/source.txt

@@ -1,3 +0,0 @@
-local_run: bbbc021_nocodazole_no_xattn_no_reweight
-checkpoint_subdir: best_model
-hf_checkpoint_name: nocodazole

nocodazole/test_samples.parquet

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