Implementation of Beta VAE for benchmarking

applications/benchmarking/DynaCLR/DINOV3/config_dinov3_convnext_tiny.yml

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+datamodule:
+  batch_size: 32
+  final_yx_patch_size:
+  - 256
+  - 256
+  include_fov_names: null
+  include_track_ids: null
+  initial_yx_patch_size:
+  - 256
+  - 256
+  normalizations:
+  - class_path: viscy.transforms.ScaleIntensityRangePercentilesd
+    init_args:
+      b_max: 1.0
+      b_min: 0.0
+      keys:
+      - RFP
+      lower: 50
+      upper: 99
+  - class_path: viscy.transforms.NormalizeIntensityd
+    init_args:
+      keys:
+      - Phase3D
+  num_workers: 10
+  source_channel:
+  - RFP
+  - Phase3D
+  z_range:
+  - 15
+  - 45
+
+embedding:
+  pca_kwargs:
+    n_components: 8
+  phate_kwargs:
+    decay: 40
+    knn: 5
+    n_components: 2
+    n_jobs: -1
+    random_state: 42
+  reductions:
+  - PHATE
+  - PCA
+
+execution:
+  overwrite: false
+  save_config: true
+  show_config: true
+
+model:
+  model_name: facebook/dinov3-convnext-tiny-pretrain-lvd1689m
+  pooling_method: mean  # Options: "mean", "max", "cls_token"
+  middle_slice_index: 18  # Specific z-slice index (if null, uses D//2)
+  channel_reduction_methods:
+    Phase3D: middle_slice
+    RFP: max
+  channel_names:
+  - RFP
+  - Phase3D
+
+paths:
+  data_path: /hpc/projects/intracellular_dashboard/organelle_dynamics/2024_02_04_A549_DENV_ZIKV_timelapse/8-train-test-split/registered_test.zarr
+  output_path: /hpc/mydata/eduardo.hirata/repos/viscy/applications/benchmarking/DynaCLR/DINOV3/embeddings_convnext_tiny_mean.zarr
+  tracks_path: /hpc/projects/intracellular_dashboard/organelle_dynamics/2024_02_04_A549_DENV_ZIKV_timelapse/8-train-test-split/track_test.zarr