Datasets:

Angelou0516
/

NucMM-Z

Exception:    SplitsNotFoundError
Message:      The split names could not be parsed from the dataset config.
Traceback:    Traceback (most recent call last):
                File "/usr/local/lib/python3.14/site-packages/datasets/inspect.py", line 286, in get_dataset_config_info
                  for split_generator in builder._split_generators(
                                         ~~~~~~~~~~~~~~~~~~~~~~~~~^
                      StreamingDownloadManager(base_path=builder.base_path, download_config=download_config)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                  )
                  ^
                File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/hdf5/hdf5.py", line 49, in _split_generators
                  import h5py
              ModuleNotFoundError: No module named 'h5py'
              
              The above exception was the direct cause of the following exception:
              
              Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/config/split_names.py", line 71, in compute_split_names_from_streaming_response
                  for split in get_dataset_split_names(
                               ~~~~~~~~~~~~~~~~~~~~~~~^
                      path=dataset,
                      ^^^^^^^^^^^^^
                      config_name=config,
                      ^^^^^^^^^^^^^^^^^^^
                      token=hf_token,
                      ^^^^^^^^^^^^^^^
                  )
                  ^
                File "/usr/local/lib/python3.14/site-packages/datasets/inspect.py", line 340, in get_dataset_split_names
                  info = get_dataset_config_info(
                      path,
                  ...<6 lines>...
                      **config_kwargs,
                  )
                File "/usr/local/lib/python3.14/site-packages/datasets/inspect.py", line 291, in get_dataset_config_info
                  raise SplitsNotFoundError("The split names could not be parsed from the dataset config.") from err
              datasets.inspect.SplitsNotFoundError: The split names could not be parsed from the dataset config.

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NucMM-Z Dataset

Overview

NucMM-Z (Neuronal Nuclei from Zebrafish) is a 3D electron microscopy (EM) dataset for nuclei instance segmentation from zebrafish brain tissue.

Property	Value
Modality	Electron Microscopy (EM)
Task	Nuclei instance segmentation
Anatomy	Zebrafish brain
Volume Size	64 × 64 × 64 voxels per patch
Train Volumes	27
Val Volumes	27
Total Size	~1.09 GB

Dataset Structure

NucMM-Z/
├── image.tif           # Full raw volume (~1 GB)
├── mask.h5             # Full annotation volume
├── README.txt          # Original readme
├── Image/
│   ├── train/          # 27 training patches (.h5)
│   └── val/            # 27 validation patches (.h5)
└── Label/
    ├── train/          # 27 training labels (.h5)
    └── val/            # 27 validation labels (.h5)

Label Format

Instance Segmentation: Each nucleus has a unique integer ID
Background: 0
Typical density: 50-300 nuclei per 64×64×64 volume

Usage with EasyMedSeg

from dataloader import NucMMZImageDataset, NucMMZVideoDataset

# Image mode (2D slices) - Recommended
dataset = NucMMZImageDataset(split='train')
sample = dataset[0]  # Returns dict with 'image' and 'mask'

# Video mode (3D volumes as frame sequences)
dataset = NucMMZVideoDataset(split='train')
video = dataset[0]  # Returns dict with 'frames' and 'masks'

Benchmark Results (SAM2)

Mode	Model	Mean Dice	Mean IoU
Image	sam2_hiera_large	0.3438	0.2566
Video	sam2_video_hiera_large	0.0631	0.0425

Recommendation: Use image mode for this dataset.

Source

Original: PyTorch Connectomics NucMM
Paper: Wei et al., MICCAI 2020

License

CC BY 4.0

Downloads last month: 10

Total file size:

1.17 GB