neuro-sam 0.1.4__tar.gz → 0.1.6__tar.gz

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Files changed (98) hide show
  1. {neuro_sam-0.1.4/src/neuro_sam.egg-info → neuro_sam-0.1.6}/PKG-INFO +1 -1
  2. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/pyproject.toml +1 -1
  3. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/napari_utils/punet_widget.py +2 -8
  4. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/punet/prob_unet_deepd3.py +3 -3
  5. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/punet/prob_unet_with_tversky.py +2 -2
  6. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/punet/punet_inference.py +1 -1
  7. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/punet/unet_blocks.py +1 -1
  8. {neuro_sam-0.1.4 → neuro_sam-0.1.6/src/neuro_sam.egg-info}/PKG-INFO +1 -1
  9. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/LICENSE +0 -0
  10. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/README.md +0 -0
  11. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/setup.cfg +0 -0
  12. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/__init__.py +0 -0
  13. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/brightest_path_lib/__init__.py +0 -0
  14. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/brightest_path_lib/algorithm/__init__.py +0 -0
  15. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/brightest_path_lib/algorithm/astar.py +0 -0
  16. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/brightest_path_lib/algorithm/waypointastar.py +0 -0
  17. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/brightest_path_lib/algorithm/waypointastar_speedup.py +0 -0
  18. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/brightest_path_lib/connected_componen.py +0 -0
  19. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/brightest_path_lib/cost/__init__.py +0 -0
  20. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/brightest_path_lib/cost/cost.py +0 -0
  21. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/brightest_path_lib/cost/reciprocal.py +0 -0
  22. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/brightest_path_lib/cost/reciprocal_transonic.py +0 -0
  23. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/brightest_path_lib/heuristic/__init__.py +0 -0
  24. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/brightest_path_lib/heuristic/euclidean.py +0 -0
  25. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/brightest_path_lib/heuristic/heuristic.py +0 -0
  26. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/brightest_path_lib/image/__init__.py +0 -0
  27. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/brightest_path_lib/image/stats.py +0 -0
  28. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/brightest_path_lib/input/__init__.py +0 -0
  29. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/brightest_path_lib/input/inputs.py +0 -0
  30. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/brightest_path_lib/node/__init__.py +0 -0
  31. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/brightest_path_lib/node/bidirectional_node.py +0 -0
  32. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/brightest_path_lib/node/node.py +0 -0
  33. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/brightest_path_lib/visualization/__init__.py +0 -0
  34. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/brightest_path_lib/visualization/flythrough.py +0 -0
  35. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/brightest_path_lib/visualization/flythrough_all.py +0 -0
  36. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/brightest_path_lib/visualization/tube_data.py +0 -0
  37. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/brightest_path_lib/visualization/tube_flythrough.py +0 -0
  38. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/napari_utils/anisotropic_scaling.py +0 -0
  39. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/napari_utils/color_utils.py +0 -0
  40. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/napari_utils/contrasting_color_system.py +0 -0
  41. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/napari_utils/main_widget.py +0 -0
  42. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/napari_utils/path_tracing_module.py +0 -0
  43. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/napari_utils/segmentation_model.py +0 -0
  44. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/napari_utils/segmentation_module.py +0 -0
  45. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/napari_utils/visualization_module.py +0 -0
  46. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/plugin.py +0 -0
  47. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/punet/__init__.py +0 -0
  48. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/punet/deepd3_model.py +0 -0
  49. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/punet/run_inference.py +0 -0
  50. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/punet/utils.py +0 -0
  51. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam.egg-info/SOURCES.txt +0 -0
  52. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam.egg-info/dependency_links.txt +0 -0
  53. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam.egg-info/entry_points.txt +0 -0
  54. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam.egg-info/requires.txt +0 -0
  55. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam.egg-info/top_level.txt +0 -0
  56. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/__init__.py +0 -0
  57. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/automatic_mask_generator.py +0 -0
  58. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/benchmark.py +0 -0
  59. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/build_sam.py +0 -0
  60. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/configs/sam2/sam2_hiera_b+.yaml +0 -0
  61. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/configs/sam2/sam2_hiera_l.yaml +0 -0
  62. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/configs/sam2/sam2_hiera_s.yaml +0 -0
  63. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/configs/sam2/sam2_hiera_t.yaml +0 -0
  64. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/configs/sam2.1/sam2.1_hiera_b+.yaml +0 -0
  65. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/configs/sam2.1/sam2.1_hiera_l.yaml +0 -0
  66. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/configs/sam2.1/sam2.1_hiera_s.yaml +0 -0
  67. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/configs/sam2.1/sam2.1_hiera_t.yaml +0 -0
  68. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/configs/sam2.1_training/sam2.1_hiera_b+_MOSE_finetune.yaml +0 -0
  69. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/configs/train.yaml +0 -0
  70. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/modeling/__init__.py +0 -0
  71. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/modeling/backbones/__init__.py +0 -0
  72. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/modeling/backbones/hieradet.py +0 -0
  73. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/modeling/backbones/image_encoder.py +0 -0
  74. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/modeling/backbones/utils.py +0 -0
  75. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/modeling/memory_attention.py +0 -0
  76. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/modeling/memory_encoder.py +0 -0
  77. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/modeling/position_encoding.py +0 -0
  78. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/modeling/sam/__init__.py +0 -0
  79. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/modeling/sam/mask_decoder.py +0 -0
  80. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/modeling/sam/prompt_encoder.py +0 -0
  81. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/modeling/sam/transformer.py +0 -0
  82. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/modeling/sam2_base.py +0 -0
  83. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/modeling/sam2_utils.py +0 -0
  84. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/sam2.1_hiera_b+.yaml +0 -0
  85. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/sam2.1_hiera_l.yaml +0 -0
  86. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/sam2.1_hiera_s.yaml +0 -0
  87. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/sam2.1_hiera_t.yaml +0 -0
  88. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/sam2_hiera_b+.yaml +0 -0
  89. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/sam2_hiera_l.yaml +0 -0
  90. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/sam2_hiera_s.yaml +0 -0
  91. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/sam2_hiera_t.yaml +0 -0
  92. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/sam2_image_predictor.py +0 -0
  93. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/sam2_video_predictor.py +0 -0
  94. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/sam2_video_predictor_legacy.py +0 -0
  95. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/utils/__init__.py +0 -0
  96. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/utils/amg.py +0 -0
  97. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/utils/misc.py +0 -0
  98. {neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/sam2/utils/transforms.py +0 -0
{neuro_sam-0.1.4/src/neuro_sam.egg-info → neuro_sam-0.1.6}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: neuro-sam
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- Version: 0.1.4
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+ Version: 0.1.6
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  Summary: Neuro-SAM: Foundation Models for Dendrite and Dendritic Spine Segmentation
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  Author-email: Nipun Arora <nipunarora8@yahoo.com>
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  License: MIT License
{neuro_sam-0.1.4 → neuro_sam-0.1.6}/pyproject.toml RENAMED
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
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  [project]
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  name = "neuro-sam"
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- version = "0.1.4"
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+ version = "0.1.6"
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  description = "Neuro-SAM: Foundation Models for Dendrite and Dendritic Spine Segmentation"
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  readme = "README.md"
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  authors = [
{neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/napari_utils/punet_widget.py RENAMED
@@ -15,14 +15,8 @@ import napari
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  from napari.qt.threading import thread_worker
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  # Import the model class
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- # Assuming running from root, so punet is a package
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- try:
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- from neuro_sam.punet.punet_inference import run_inference_volume
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- except ImportError:
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- # Fallback if running from a different context, try to append path
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- import sys
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- sys.path.append(os.path.join(os.path.dirname(__file__), '..', 'punet'))
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- from neuro_sam.punet_inference import run_inference_volume
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+ # Assumes installed package structure
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+ from neuro_sam.punet.punet_inference import run_inference_volume
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{neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/punet/prob_unet_deepd3.py RENAMED
@@ -10,9 +10,9 @@ import torch.nn.functional as F
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  from torch.distributions import Normal, Independent, kl
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  import numpy as np
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- from deepd3_model import DeepD3Model
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- from unet_blocks import *
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- from utils import init_weights, init_weights_orthogonal_normal, l2_regularisation
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+ from .deepd3_model import DeepD3Model
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+ from .unet_blocks import *
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+ from .utils import init_weights, init_weights_orthogonal_normal, l2_regularisation
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  device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
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{neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/punet/prob_unet_with_tversky.py RENAMED
@@ -12,8 +12,8 @@ import torch
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  import torch.nn as nn
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  import torch.nn.functional as F
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  from torch.distributions import kl
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- from deepd3_model import DeepD3Model
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- from prob_unet_deepd3 import AxisAlignedConvGaussian, Fcomb
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+ from .deepd3_model import DeepD3Model
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+ from .prob_unet_deepd3 import AxisAlignedConvGaussian, Fcomb
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  class TverskyLoss(nn.Module):
{neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/punet/punet_inference.py RENAMED
@@ -7,7 +7,7 @@ import torch
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  import tifffile as tiff
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  from tqdm import tqdm
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- from prob_unet_with_tversky import ProbabilisticUnetDualLatent
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+ from .prob_unet_with_tversky import ProbabilisticUnetDualLatent
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  def pad_to_multiple(img: np.ndarray, multiple: int = 32):
{neuro_sam-0.1.4 → neuro_sam-0.1.6}/src/neuro_sam/punet/unet_blocks.py RENAMED
@@ -2,7 +2,7 @@ import torch
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  import torch.nn as nn
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  from torch.autograd import Variable
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  import numpy as np
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- from utils import init_weights
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+ from .utils import init_weights
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  class DownConvBlock(nn.Module):
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  """
{neuro_sam-0.1.4 → neuro_sam-0.1.6/src/neuro_sam.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: neuro-sam
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- Version: 0.1.4
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+ Version: 0.1.6
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  Summary: Neuro-SAM: Foundation Models for Dendrite and Dendritic Spine Segmentation
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  Author-email: Nipun Arora <nipunarora8@yahoo.com>
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  License: MIT License
{neuro_sam-0.1.4 → neuro_sam-0.1.6}/LICENSE RENAMED
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{neuro_sam-0.1.4 → neuro_sam-0.1.6}/README.md RENAMED
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{neuro_sam-0.1.4 → neuro_sam-0.1.6}/setup.cfg RENAMED
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