Dataset: Segmentation of cortical bone, trabecular bone, and medullary pores from micro-CT images using 2D and 3D deep learning models
Data files
Jan 22, 2025 version files 72.77 GB
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_composite.zip
22.37 GB
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_Models.zip
838.01 MB
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_Scripts.zip
1.50 KB
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BM_78743_FTFi.zip
3.74 GB
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BM_81969_FTFi.zip
3.97 GB
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BM_81969_HRU.zip
5.06 GB
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README.md
26.09 KB
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SNM_44262_HRU.zip
2.09 GB
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SNM_53994_FTFi.zip
3.77 GB
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SNM_53994_HRU.zip
2.50 GB
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UAM_24789_FTFi.zip
4.74 GB
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UAM_67696_HF.zip
8.13 GB
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UAM_67696_TFiRU.zip
4.36 GB
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UF_23593-24550_HF.zip
6.70 GB
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UF_24550_TFiRU.zip
2.32 GB
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UF_31151_HRU.zip
2.18 GB
Abstract
Computed tomography (CT) enables rapid imaging of large-scale studies of bone, but those datasets typically require manual segmentation, which is time-consuming and prone to error. Convolutional neural networks (CNNs) offer an automated solution, achieving superior performance on image data. Here, we used CNNs to train segmentation models from scratch on 2D and 3D patches from micro-CT scans of otter long bones. These new models, collectively called BONe (Bone One-shot Network), aimed to be fast and accurate, and we expected enhanced results from 3D training due to better spatial context. Our results showed that 3D training required substantially more memory. Contrary to expectations, 2D models performed slightly better than 3D models in labeling details such as thin trabecular bone. Although lacking in some detail, 3D models appeared to generalize better and predict smoother internal surfaces than 2D models. However, the massive computational costs of 3D models limit their scalability and practicality, leading us to recommend 2D models for bone segmentation. BONe models showed potential for broader applications with variation in performance across species and scan quality. Notably, BONe models demonstrated promising results on skull segmentation, suggesting their potential utility beyond long bones with further refinement and fine-tuning.
README: Dataset: Segmentation of cortical bone, trabecular bone, and medullary pores from micro-CT images using 2D and 3D deep learning models
https://doi.org/10.5061/dryad.b2rbnzsq4
Introduction: The following document outlines the structure of data repository.
“_composite.zip” contains separate folders for the raw micro-CT slices and CTP labels used for model fitting. Because Avizo’s deep learning segmentation module can only load a single pair of data files (i.e., one file consists of the raw slices and the second file consists of the labels), we appended the samples used for fitting into a composite sample.
“_Models.zip” contains the deep learning models for bone-pore and cortical-trabecular-pores segmentation. Model files are intended for use in the commercial software Avizo/Amira but are compatible with a variety of both open source and commercial software (e.g., TensorFlow or Comet Dragonfly). Files consist of model weights (HDF5 format), network architecture (JSON format), and processing code (PY format).
“_Scripts.zip” contains the Avizo script files to compare overlap accuracy between reference and predicted segmentations (IoU Score). The script is installed by copying the two files into Avizo/Amira’s “share/script-objects” folder before starting Avizo/Amira. Once installed, the script (IOUScore) can be found in the menu of modules under the Compute category.
The remaining zip files contain raw slice data (.tif), scanning metadata (.xtekct & .info that can be opened by a text editor), and reference and predicted segmentations (.tif) for each of the 12 volumes in the deep learning sample. Samples used for training and validation are stored in the “Fitting” folder, whereas samples used for independent evaluation of models are stored in the “Testing” folder. To maintain data transparency, minor background artifacts were not removed from predicted segmentations to accurately represent model output.
Directory of file structure
_composite.zip\
|- Data\
|- |- Fitting\
|- |- |- _composite\
|- |- |- |- _Raw\
|- |- |- |- |- composite_.info\
|- |- |- |- |- composite_0000.tif\
|- |- |- |- |- composite_XXXX.tif\
|- |- |- |- |- composite_7679.tif\
|- |- |- |- CTP-label\
|- |- |- |- |- composite_cort-trab-pores-label_v2_.info\
|- |- |- |- |- composite_cort-trab-pores-label_v2_0000.tif\
|- |- |- |- |- composite_cort-trab-pores-label_v2_XXXX.tif\
|- |- |- |- |- composite_cort-trab-pores-label_v2_7679.tif
_Models.zip\
|- BP-2D-02\
|- |- BP-2D-02.hdf5\
|- |- BP-2D-02.json\
|- |- BP-2D-02.py\
|- BP-2D-02a\
|- |- BP-2D-02a.hdf5\
|- |- BP-2D-02a.json\
|- |- BP-2D-02a.py\
|- BP-3D-02\
|- |- BP-3D-02.hdf5\
|- |- BP-3D-02.json\
|- |- BP-3D-02.py\
|- BP-3D-02a\
|- |- BP-3D-02a.hdf5\
|- |- BP-3D-02a.json\
|- |- BP-3D-02a.py\
|- CTP-2D-02\
|- |- CTP-2D-02.hdf5\
|- |- CTP-2D-02.json\
|- |- CTP-2D-02.py\
|- CTP-2D-02a\
|- |- CTP-2D-02a.hdf5\
|- |- CTP-2D-02a.json\
|- |- CTP-2D-02a.py\
|- CTP-3D-02\
|- |- CTP-3D-02.hdf5\
|- |- CTP-3D-02.json\
|- |- CTP-3D-02.py\
|- CTP-3D-02a\
|- |- CTP-3D-02a.hdf5\
|- |- CTP-3D-02a.json\
|- |- CTP-3D-02a.py
_Scripts.zip\
|- IOUScore.rc\
|- IOUScore.scro
BM_78743_FTFi.zip\
|- Data\
|- |- Fitting\
|- |- |- BM_78743_FTFi\
|- |- |- |- _Raw\
|- |- |- |- |- _BM_78743_FTFi.xtekct\
|- |- |- |- |- BM_78743_FTFi_.info\
|- |- |- |- |- BM_78743_FTFi_0000.tif\
|- |- |- |- |- BM_78743_FTFi_XXXX.tif\
|- |- |- |- |- BM_78743_FTFi_2047.tif\
|- |- |- |- CTP-label\
|- |- |- |- |- _BM_78743_FTFi.xtekct\
|- |- |- |- |- BM_78743_FTFi_cort-trab-pores-label_v2_.info\
|- |- |- |- |- BM_78743_FTFi_cort-trab-pores-label_v2_0000.tif\
|- |- |- |- |- BM_78743_FTFi_cort-trab-pores-label_v2_XXXX.tif\
|- |- |- |- |- BM_78743_FTFi_cort-trab-pores-label_v2_2047.tif\
|- |- |- |- Predict_BP-2D-02a\
|- |- |- |- |- _BM_78743_FTFi.xtekct\
|- |- |- |- |- BM_78743_FTFi_predict_BP-2D-02a_.info\
|- |- |- |- |- BM_78743_FTFi_predict_BP-2D-02a_0000.tif\
|- |- |- |- |- BM_78743_FTFi_predict_BP-2D-02a_XXXX.tif\
|- |- |- |- |- BM_78743_FTFi_predict_BP-2D-02a_2047.tif\
|- |- |- |- Predict_BP-3D-02a\
|- |- |- |- |- _BM_78743_FTFi.xtekct\
|- |- |- |- |- BM_78743_FTFi_predict_BP-3D-02a_.info\
|- |- |- |- |- BM_78743_FTFi_predict_BP-3D-02a_0000.tif\
|- |- |- |- |- BM_78743_FTFi_predict_BP-3D-02a_XXXX.tif\
|- |- |- |- |- BM_78743_FTFi_predict_BP-3D-02a_2047.tif\
|- |- |- |- Predict_CTP-2D-02a\
|- |- |- |- |- _BM_78743_FTFi.xtekct\
|- |- |- |- |- BM_78743_FTFi_predict_CTP-2D-02a_.info\
|- |- |- |- |- BM_78743_FTFi_predict_CTP-2D-02a_0000.tif\
|- |- |- |- |- BM_78743_FTFi_predict_CTP-2D-02a_XXXX.tif\
|- |- |- |- |- BM_78743_FTFi_predict_CTP-2D-02a_2047.tif\
|- |- |- |- Predict_CTP-3D-02a\
|- |- |- |- |- _BM_78743_FTFi.xtekct\
|- |- |- |- |- BM_78743_FTFi_predict_CTP-3D-02a_.info\
|- |- |- |- |- BM_78743_FTFi_predict_CTP-3D-02a_0000.tif\
|- |- |- |- |- BM_78743_FTFi_predict_CTP-3D-02a_XXXX.tif\
|- |- |- |- |- BM_78743_FTFi_predict_CTP-3D-02a_2047.tif
BM_81969_FTFi.zip\
|- Data\
|- |- Testing\
|- |- |- BM_81969_FTFi\
|- |- |- |- _Raw\
|- |- |- |- |- _BM_81969_FTFi.xtekct\
|- |- |- |- |- BM_81969_FTFi_.info\
|- |- |- |- |- BM_81969_FTFi_0000.tif\
|- |- |- |- |- BM_81969_FTFi_XXXX.tif\
|- |- |- |- |- BM_81969_FTFi_2194.tif\
|- |- |- |- CTP-label\
|- |- |- |- |- _BM_81969_FTFi.xtekct\
|- |- |- |- |- BM_81969_FTFi_cort-trab-pores-label_.info\
|- |- |- |- |- BM_81969_FTFi_cort-trab-pores-label_0000.tif\
|- |- |- |- |- BM_81969_FTFi_cort-trab-pores-label_XXXX.tif\
|- |- |- |- |- BM_81969_FTFi_cort-trab-pores-label_2194.tif\
|- |- |- |- Predict_BP-2D-02a\
|- |- |- |- |- _BM_81969_FTFi.xtekct\
|- |- |- |- |- BM_81969_FTFi_predict_BP-2D-02a_.info\
|- |- |- |- |- BM_81969_FTFi_predict_BP-2D-02a_0000.tif\
|- |- |- |- |- BM_81969_FTFi_predict_BP-2D-02a_XXXX.tif\
|- |- |- |- |- BM_81969_FTFi_predict_BP-2D-02a_2194.tif\
|- |- |- |- Predict_BP-3D-02a\
|- |- |- |- |- _BM_81969_FTFi.xtekct\
|- |- |- |- |- BM_81969_FTFi_predict_BP-3D-02a_.info\
|- |- |- |- |- BM_81969_FTFi_predict_BP-3D-02a_0000.tif\
|- |- |- |- |- BM_81969_FTFi_predict_BP-3D-02a_XXXX.tif\
|- |- |- |- |- BM_81969_FTFi_predict_BP-3D-02a_2194.tif\
|- |- |- |- Predict_CTP-2D-02a\
|- |- |- |- |- _BM_81969_FTFi.xtekct\
|- |- |- |- |- BM_81969_FTFi_predict_CTP-2D-02a_.info\
|- |- |- |- |- BM_81969_FTFi_predict_CTP-2D-02a_0000.tif\
|- |- |- |- |- BM_81969_FTFi_predict_CTP-2D-02a_XXXX.tif\
|- |- |- |- |- BM_81969_FTFi_predict_CTP-2D-02a_2194.tif\
|- |- |- |- Predict_CTP-3D-02a\
|- |- |- |- |- _BM_81969_FTFi.xtekct\
|- |- |- |- |- BM_81969_FTFi_predict_CTP-3D-02a_.info\
|- |- |- |- |- BM_81969_FTFi_predict_CTP-3D-02a_0000.tif\
|- |- |- |- |- BM_81969_FTFi_predict_CTP-3D-02a_XXXX.tif\
|- |- |- |- |- BM_81969_FTFi_predict_CTP-3D-02a_2194.tif
BM_81969_HRU.zip\
|- Data\
|- |- Testing\
|- |- |- BM_81969_HRU\
|- |- |- |- _Raw\
|- |- |- |- |- _BM_81969_HRU.xtekct\
|- |- |- |- |- BM_81969_HRU_.info\
|- |- |- |- |- BM_81969_HRU_0000.tif\
|- |- |- |- |- BM_81969_HRU_XXXX.tif\
|- |- |- |- |- BM_81969_HRU_1994.tif\
|- |- |- |- CTP-label\
|- |- |- |- |- _BM_81969_HRU.xtekct\
|- |- |- |- |- BM_81969_HRU_cort-trab-pores-label_v2_.info\
|- |- |- |- |- BM_81969_HRU_cort-trab-pores-label_v2_0000.tif\
|- |- |- |- |- BM_81969_HRU_cort-trab-pores-label_v2_XXXX.tif\
|- |- |- |- |- BM_81969_HRU_cort-trab-pores-label_v2_1994.tif\
|- |- |- |- Predict_BP-2D-02a\
|- |- |- |- |- _BM_81969_HRU.xtekct\
|- |- |- |- |- BM_81969_HRU_predict_BP-2D-02a_.info\
|- |- |- |- |- BM_81969_HRU_predict_BP-2D-02a_0000.tif\
|- |- |- |- |- BM_81969_HRU_predict_BP-2D-02a_XXXX.tif\
|- |- |- |- |- BM_81969_HRU_predict_BP-2D-02a_1994.tif\
|- |- |- |- Predict_BP-3D-02a\
|- |- |- |- |- _BM_81969_HRU.xtekct\
|- |- |- |- |- BM_81969_HRU_predict_BP-3D-02a_.info\
|- |- |- |- |- BM_81969_HRU_predict_BP-3D-02a_0000.tif\
|- |- |- |- |- BM_81969_HRU_predict_BP-3D-02a_XXXX.tif\
|- |- |- |- |- BM_81969_HRU_predict_BP-3D-02a_1994.tif\
|- |- |- |- Predict_CTP-2D-02a\
|- |- |- |- |- _BM_81969_HRU.xtekct\
|- |- |- |- |- BM_81969_HRU_predict_CTP-2D-02a_.info\
|- |- |- |- |- BM_81969_HRU_predict_CTP-2D-02a_0000.tif\
|- |- |- |- |- BM_81969_HRU_predict_CTP-2D-02a_XXXX.tif\
|- |- |- |- |- BM_81969_HRU_predict_CTP-2D-02a_1994.tif\
|- |- |- |- Predict_CTP-3D-02a\
|- |- |- |- |- _BM_81969_HRU.xtekct\
|- |- |- |- |- BM_81969_HRU_predict_CTP-3D-02a_.info\
|- |- |- |- |- BM_81969_HRU_predict_CTP-3D-02a_0000.tif\
|- |- |- |- |- BM_81969_HRU_predict_CTP-3D-02a_XXXX.tif\
|- |- |- |- |- BM_81969_HRU_predict_CTP-3D-02a_1994.tif
SNM_44262_HRU.zip\
|- Data\
|- |- Fitting\
|- |- |- SNM_44262_HRU\
|- |- |- |- _Raw\
|- |- |- |- |- _SNM_44262_HRU.xtekct\
|- |- |- |- |- SNM_44262_HRU_.info\
|- |- |- |- |- SNM_44262_HRU_0000.tif\
|- |- |- |- |- SNM_44262_HRU_XXXX.tif\
|- |- |- |- |- SNM_44262_HRU_1535.tif\
|- |- |- |- CTP-label\
|- |- |- |- |- _SNM_44262_HRU.xtekct\
|- |- |- |- |- SNM_44262_HRU_cort-trab-pores-label_v2_.info\
|- |- |- |- |- SNM_44262_HRU_cort-trab-pores-label_v2_0000.tif\
|- |- |- |- |- SNM_44262_HRU_cort-trab-pores-label_v2_XXXX.tif\
|- |- |- |- |- SNM_44262_HRU_cort-trab-pores-label_v2_1535.tif\
|- |- |- |- Predict_BP-2D-02a\
|- |- |- |- |- _SNM_44262_HRU.xtekct\
|- |- |- |- |- SNM_44262_HRU_predict_BP-2D-02a_.info\
|- |- |- |- |- SNM_44262_HRU_predict_BP-2D-02a_0000.tif\
|- |- |- |- |- SNM_44262_HRU_predict_BP-2D-02a_XXXX.tif\
|- |- |- |- |- SNM_44262_HRU_predict_BP-2D-02a_1535.tif\
|- |- |- |- Predict_BP-3D-02a\
|- |- |- |- |- _SNM_44262_HRU.xtekct\
|- |- |- |- |- SNM_44262_HRU_predict_BP-3D-02a_.info\
|- |- |- |- |- SNM_44262_HRU_predict_BP-3D-02a_0000.tif\
|- |- |- |- |- SNM_44262_HRU_predict_BP-3D-02a_XXXX.tif\
|- |- |- |- |- SNM_44262_HRU_predict_BP-3D-02a_1535.tif\
|- |- |- |- Predict_CTP-2D-02a\
|- |- |- |- |- _SNM_44262_HRU.xtekct\
|- |- |- |- |- SNM_44262_HRU_predict_CTP-2D-02a_.info\
|- |- |- |- |- SNM_44262_HRU_predict_CTP-2D-02a_0000.tif\
|- |- |- |- |- SNM_44262_HRU_predict_CTP-2D-02a_XXXX.tif\
|- |- |- |- |- SNM_44262_HRU_predict_CTP-2D-02a_1535.tif\
|- |- |- |- Predict_CTP-3D-02a\
|- |- |- |- |- _SNM_44262_HRU.xtekct\
|- |- |- |- |- SNM_44262_HRU_predict_CTP-3D-02a_.info\
|- |- |- |- |- SNM_44262_HRU_predict_CTP-3D-02a_0000.tif\
|- |- |- |- |- SNM_44262_HRU_predict_CTP-3D-02a_XXXX.tif\
|- |- |- |- |- SNM_44262_HRU_predict_CTP-3D-02a_1535.tif
SNM_53994_FTFi.zip\
|- Data\
|- |- Fitting\
|- |- |- SNM_53994_FTFi\
|- |- |- |- _Raw\
|- |- |- |- |- _SNM_53994_FTFi.xtekct\
|- |- |- |- |- SNM_53994_FTFi_.info\
|- |- |- |- |- SNM_53994_FTFi_0000.tif\
|- |- |- |- |- SNM_53994_FTFi_XXXX.tif\
|- |- |- |- |- SNM_53994_FTFi_2175.tif\
|- |- |- |- CTP-label\
|- |- |- |- |- _SNM_53994_FTFi.xtekct\
|- |- |- |- |- SNM_53994_FTFi_cort-trab-pores-label_v2a_.info\
|- |- |- |- |- SNM_53994_FTFi_cort-trab-pores-label_v2a_0000.tif\
|- |- |- |- |- SNM_53994_FTFi_cort-trab-pores-label_v2a_XXXX.tif\
|- |- |- |- |- SNM_53994_FTFi_cort-trab-pores-label_v2a_2175.tif\
|- |- |- |- Predict_BP-2D-02a\
|- |- |- |- |- _SNM_53994_FTFi.xtekct\
|- |- |- |- |- SNM_53994_FTFi_predict_BP-2D-02a_.info\
|- |- |- |- |- SNM_53994_FTFi_predict_BP-2D-02a_0000.tif\
|- |- |- |- |- SNM_53994_FTFi_predict_BP-2D-02a_XXXX.tif\
|- |- |- |- |- SNM_53994_FTFi_predict_BP-2D-02a_2175.tif\
|- |- |- |- Predict_BP-3D-02a\
|- |- |- |- |- _SNM_53994_FTFi.xtekct\
|- |- |- |- |- SNM_53994_FTFi_predict_BP-3D-02a_.info\
|- |- |- |- |- SNM_53994_FTFi_predict_BP-3D-02a_0000.tif\
|- |- |- |- |- SNM_53994_FTFi_predict_BP-3D-02a_XXXX.tif\
|- |- |- |- |- SNM_53994_FTFi_predict_BP-3D-02a_2175.tif\
|- |- |- |- Predict_CTP-2D-02a\
|- |- |- |- |- _SNM_53994_FTFi.xtekct\
|- |- |- |- |- SNM_53994_FTFi_predict_CTP-2D-02a_.info\
|- |- |- |- |- SNM_53994_FTFi_predict_CTP-2D-02a_0000.tif\
|- |- |- |- |- SNM_53994_FTFi_predict_CTP-2D-02a_XXXX.tif\
|- |- |- |- |- SNM_53994_FTFi_predict_CTP-2D-02a_2175.tif\
|- |- |- |- Predict_CTP-3D-02a\
|- |- |- |- |- _SNM_53994_FTFi.xtekct\
|- |- |- |- |- SNM_53994_FTFi_predict_CTP-3D-02a_.info\
|- |- |- |- |- SNM_53994_FTFi_predict_CTP-3D-02a_0000.tif\
|- |- |- |- |- SNM_53994_FTFi_predict_CTP-3D-02a_XXXX.tif\
|- |- |- |- |- SNM_53994_FTFi_predict_CTP-3D-02a_2175.tif
SNM_53994_HRU.zip\
|- Data\
|- |- Testing\
|- |- |- SNM_53994_HRU\
|- |- |- |- _Raw\
|- |- |- |- |- _SNM_53994_HRU.xtekct\
|- |- |- |- |- SNM_53994_HRU_.info\
|- |- |- |- |- SNM_53994_HRU_0000.tif\
|- |- |- |- |- SNM_53994_HRU_XXXX.tif\
|- |- |- |- |- SNM_53994_HRU_1808.tif\
|- |- |- |- CTP-label\
|- |- |- |- |- _SNM_53994_HRU.xtekct\
|- |- |- |- |- SNM_53994_HRU_cort-trab-pores-label_.info\
|- |- |- |- |- SNM_53994_HRU_cort-trab-pores-label_0000.tif\
|- |- |- |- |- SNM_53994_HRU_cort-trab-pores-label_XXXX.tif\
|- |- |- |- |- SNM_53994_HRU_cort-trab-pores-label_1808.tif\
|- |- |- |- Predict_BP-2D-02a\
|- |- |- |- |- _SNM_53994_HRU.xtekct\
|- |- |- |- |- SNM_53994_HRU_predict_BP-2D-02a_.info\
|- |- |- |- |- SNM_53994_HRU_predict_BP-2D-02a_0000.tif\
|- |- |- |- |- SNM_53994_HRU_predict_BP-2D-02a_XXXX.tif\
|- |- |- |- |- SNM_53994_HRU_predict_BP-2D-02a_1808.tif\
|- |- |- |- Predict_BP-3D-02a\
|- |- |- |- |- _SNM_53994_HRU.xtekct\
|- |- |- |- |- SNM_53994_HRU_predict_BP-3D-02a_.info\
|- |- |- |- |- SNM_53994_HRU_predict_BP-3D-02a_0000.tif\
|- |- |- |- |- SNM_53994_HRU_predict_BP-3D-02a_XXXX.tif\
|- |- |- |- |- SNM_53994_HRU_predict_BP-3D-02a_1808.tif\
|- |- |- |- Predict_CTP-2D-02a\
|- |- |- |- |- _SNM_53994_HRU.xtekct\
|- |- |- |- |- SNM_53994_HRU_predict_CTP-2D-02a_.info\
|- |- |- |- |- SNM_53994_HRU_predict_CTP-2D-02a_0000.tif\
|- |- |- |- |- SNM_53994_HRU_predict_CTP-2D-02a_XXXX.tif\
|- |- |- |- |- SNM_53994_HRU_predict_CTP-2D-02a_1808.tif\
|- |- |- |- Predict_CTP-3D-02a\
|- |- |- |- |- _SNM_53994_HRU.xtekct\
|- |- |- |- |- SNM_53994_HRU_predict_CTP-3D-02a_.info\
|- |- |- |- |- SNM_53994_HRU_predict_CTP-3D-02a_0000.tif\
|- |- |- |- |- SNM_53994_HRU_predict_CTP-3D-02a_XXXX.tif\
|- |- |- |- |- SNM_53994_HRU_predict_CTP-3D-02a_1808.tif
UAM_24789_FTFi.zip\
|- Data\
|- |- Testing\
|- |- |- UAM_24789_FTFi\
|- |- |- |- _Raw\
|- |- |- |- |- _UAM_24789_FTFi.xtekct\
|- |- |- |- |- UAM_24789_FTFi_.info\
|- |- |- |- |- UAM_24789_FTFi_0000.tif\
|- |- |- |- |- UAM_24789_FTFi_XXXX.tif\
|- |- |- |- |- UAM_24789_FTFi_2097.tif\
|- |- |- |- CTP-label\
|- |- |- |- |- _UAM_24789_FTFi_HF.xtekct\
|- |- |- |- |- UAM_24789_FTFi_cort-trab-pores-label _.info\
|- |- |- |- |- UAM_24789_FTFi_cort-trab-pores-label_0000.tif\
|- |- |- |- |- UAM_24789_FTFi_cort-trab-pores-label_XXXX.tif\
|- |- |- |- |- UAM_24789_FTFi_cort-trab-pores-label_2097.tif\
|- |- |- |- Predict_BP-2D-02a\
|- |- |- |- |- _UAM_24789_FTFi.xtekct\
|- |- |- |- |- UAM_24789_FTFi_predict_BP-2D-02a_.info\
|- |- |- |- |- UAM_24789_FTFi_predict_BP-2D-02a_0000.tif\
|- |- |- |- |- UAM_24789_FTFi_predict_BP-2D-02a_XXXX.tif\
|- |- |- |- |- UAM_24789_FTFi_predict_BP-2D-02a_2097.tif\
|- |- |- |- Predict_BP-3D-02a\
|- |- |- |- |- _UAM_24789_FTFi.xtekct\
|- |- |- |- |- UAM_24789_FTFi_predict_BP-3D-02a_.info\
|- |- |- |- |- UAM_24789_FTFi_predict_BP-3D-02a_0000.tif\
|- |- |- |- |- UAM_24789_FTFi_predict_BP-3D-02a_XXXX.tif\
|- |- |- |- |- UAM_24789_FTFi_predict_BP-3D-02a_2097.tif\
|- |- |- |- Predict_CTP-2D-02a\
|- |- |- |- |- _UAM_24789_FTFi.xtekct\
|- |- |- |- |- UAM_24789_FTFi_predict_CTP-2D-02a_.info\
|- |- |- |- |- UAM_24789_FTFi_predict_CTP-2D-02a_0000.tif\
|- |- |- |- |- UAM_24789_FTFi_predict_CTP-2D-02a_XXXX.tif\
|- |- |- |- |- UAM_24789_FTFi_predict_CTP-2D-02a_2097.tif\
|- |- |- |- Predict_CTP-3D-02a\
|- |- |- |- |- _UAM_24789_FTFi.xtekct\
|- |- |- |- |- UAM_24789_FTFi_predict_CTP-3D-02a_.info\
|- |- |- |- |- UAM_24789_FTFi_predict_CTP-3D-02a_0000.tif|\
|- |- |- |- |- UAM_24789_FTFi_predict_CTP-3D-02a_XXXX.tif\
|- |- |- |- |- UAM_24789_FTFi_predict_CTP-3D-02a_2097.tif
UAM_67696_HF.zip\
|- Data\
|- |- Fitting\
|- |- |- UAM_67696_HF\
|- |- |- |- _Raw\
|- |- |- |- |- _UAM_67696_HF.xtekct\
|- |- |- |- |- UAM_67696_HF_.info\
|- |- |- |- |- UAM_67696_HF_0000.tif\
|- |- |- |- |- UAM_67696_HF_XXXX.tif\
|- |- |- |- |- UAM_67696_HF_1535.tif\
|- |- |- |- CTP-label\
|- |- |- |- |- _UAM_67696_HF.xtekct\
|- |- |- |- |- UAM_67696_HF_cort-trab-pores-label_v2a_.info\
|- |- |- |- |- UAM_67696_HF_cort-trab-pores-label_v2a_0000.tif\
|- |- |- |- |- UAM_67696_HF_cort-trab-pores-label_v2a_XXXX.tif\
|- |- |- |- |- UAM_67696_HF_cort-trab-pores-label_v2a_1535.tif\
|- |- |- |- Predict_BP-2D-02a\
|- |- |- |- |- _UAM_67696_HF.xtekct\
|- |- |- |- |- UAM_67696_HF_predict_BP-2D-02a_.info\
|- |- |- |- |- UAM_67696_HF_predict_BP-2D-02a_0000.tif\
|- |- |- |- |- UAM_67696_HF_predict_BP-2D-02a_XXXX.tif\
|- |- |- |- |- UAM_67696_HF_predict_BP-2D-02a_1535.tif\
|- |- |- |- Predict_BP-3D-02a\
|- |- |- |- |- _UAM_67696_HF.xtekct\
|- |- |- |- |- UAM_67696_HF_predict_BP-3D-02a_.info\
|- |- |- |- |- UAM_67696_HF_predict_BP-3D-02a_0000.tif\
|- |- |- |- |- UAM_67696_HF_predict_BP-3D-02a_XXXX.tif\
|- |- |- |- |- UAM_67696_HF_predict_BP-3D-02a_1535.tif\
|- |- |- |- Predict_CTP-2D-02a\
|- |- |- |- |- _UAM_67696_HF.xtekct\
|- |- |- |- |- UAM_67696_HF_predict_CTP-2D-02a_.info\
|- |- |- |- |- UAM_67696_HF_predict_CTP-2D-02a_0000.tif\
|- |- |- |- |- UAM_67696_HF_predict_CTP-2D-02a_XXXX.tif\
|- |- |- |- |- UAM_67696_HF_predict_CTP-2D-02a_1535.tif\
|- |- |- |- Predict_CTP-3D-02a\
|- |- |- |- |- _UAM_67696_HF.xtekct\
|- |- |- |- |- UAM_67696_HF_predict_CTP-3D-02a_.info\
|- |- |- |- |- UAM_67696_HF_predict_CTP-3D-02a_0000.tif\
|- |- |- |- |- UAM_67696_HF_predict_CTP-3D-02a_XXXX.tif\
|- |- |- |- |- UAM_67696_HF_predict_CTP-3D-02a_1535.tif
UAM_67696_TFiRU.zip\
|- Data\
|- |- Fitting\
|- |- |- UAM_67696_TFiRU\
|- |- |- |- _Raw\
|- |- |- |- |- _UAM_67696_TFiRU.xtekct\
|- |- |- |- |- UAM_67696_TFiRU_.info\
|- |- |- |- |- UAM_67696_TFiRU_0000.tif\
|- |- |- |- |- UAM_67696_TFiRU_XXXX.tif\
|- |- |- |- |- UAM_67696_TFiRU_2320.tif\
|- |- |- |- CTP-label\
|- |- |- |- |- _UAM_67696_TFiRU.xtekct\
|- |- |- |- |- UAM_67696_TFiRU_cort-trab-pores-label_v2_.info\
|- |- |- |- |- UAM_67696_TFiRU_cort-trab-pores-label_v2_0000.tif\
|- |- |- |- |- UAM_67696_TFiRU_cort-trab-pores-label_v2_XXXX.tif\
|- |- |- |- |- UAM_67696_TFiRU_cort-trab-pores-label_v2_2320.tif\
|- |- |- |- Predict_BP-2D-02a\
|- |- |- |- |- _UAM_67696_TFiRU.xtekct\
|- |- |- |- |- UAM_67696_TFiRU_predict_BP-2D-02a_.info\
|- |- |- |- |- UAM_67696_TFiRU_predict_BP-2D-02a_0000.tif\
|- |- |- |- |- UAM_67696_TFiRU_predict_BP-2D-02a_XXXX.tif\
|- |- |- |- |- UAM_67696_TFiRU_predict_BP-2D-02a_2320.tif\
|- |- |- |- Predict_BP-3D-02a\
|- |- |- |- |- _UAM_67696_TFiRU.xtekct\
|- |- |- |- |- UAM_67696_TFiRU_predict_BP-3D-02a_.info\
|- |- |- |- |- UAM_67696_TFiRU_predict_BP-3D-02a_0000.tif\
|- |- |- |- |- UAM_67696_TFiRU_predict_BP-3D-02a_XXXX.tif\
|- |- |- |- |- UAM_67696_TFiRU_predict_BP-3D-02a_2320.tif\
|- |- |- |- Predict_CTP-2D-02a\
|- |- |- |- |- _UAM_67696_TFiRU.xtekct\
|- |- |- |- |- UAM_67696_TFiRU_predict_CTP-2D-02a_.info\
|- |- |- |- |- UAM_67696_TFiRU_predict_CTP-2D-02a_0000.tif\
|- |- |- |- |- UAM_67696_TFiRU_predict_CTP-2D-02a_XXXX.tif\
|- |- |- |- |- UAM_67696_TFiRU_predict_CTP-2D-02a_2320.tif\
|- |- |- |- Predict_CTP-3D-02a\
|- |- |- |- |- _UAM_67696_TFiRU.xtekct\
|- |- |- |- |- UAM_67696_TFiRU_predict_CTP-3D-02a_.info\
|- |- |- |- |- UAM_67696_TFiRU_predict_CTP-3D-02a_0000.tif\
|- |- |- |- |- UAM_67696_TFiRU_predict_CTP-3D-02a_XXXX.tif\
|- |- |- |- |- UAM_67696_TFiRU_predict_CTP-3D-02a_2320.tif
UF_23593-24550_HF.zip\
|- Data\
|- |- Fitting\
|- |- |- UF_23593-24550_HF\
|- |- |- |- _Raw\
|- |- |- |- |- _UF_23593-24550_HF.xtekct\
|- |- |- |- |- UF_23593-24550_HF_.info\
|- |- |- |- |- UF_23593-24550_HF_0000.tif\
|- |- |- |- |- UF_23593-24550_HF_XXXX.tif\
|- |- |- |- |- UF_23593-24550_HF_1663.tif\
|- |- |- |- CTP-label\
|- |- |- |- |- _UF_23593-24550_HF.xtekct\
|- |- |- |- |- UF_23593-24550_HF_cort-trab-pores-label_v2_.info\
|- |- |- |- |- UF_23593-24550_HF_cort-trab-pores-label_v2_0000.tif\
|- |- |- |- |- UF_23593-24550_HF_cort-trab-pores-label_v2_XXXX.tif\
|- |- |- |- |- UF_23593-24550_HF_cort-trab-pores-label_v2_1663.tif\
|- |- |- |- Predict_BP-2D-02a\
|- |- |- |- |- _UF_23593-24550_HF.xtekct\
|- |- |- |- |- UF_23593-24550_HF_predict_BP-2D-02a_.info\
|- |- |- |- |- UF_23593-24550_HF_predict_BP-2D-02a_0000.tif\
|- |- |- |- |- UF_23593-24550_HF_predict_BP-2D-02a_XXXX.tif\
|- |- |- |- |- UF_23593-24550_HF_predict_BP-2D-02a_1663.tif\
|- |- |- |- Predict_BP-3D-02a\
|- |- |- |- |- _UF_23593-24550_HF.xtekct\
|- |- |- |- |- UF_23593-24550_HF_predict_BP-3D-02a_.info\
|- |- |- |- |- UF_23593-24550_HF_predict_BP-3D-02a_0000.tif\
|- |- |- |- |- UF_23593-24550_HF_predict_BP-3D-02a_XXXX.tif\
|- |- |- |- |- UF_23593-24550_HF_predict_BP-3D-02a_1663.tif\
|- |- |- |- Predict_CTP-2D-02a\
|- |- |- |- |- _UF_23593-24550_HF.xtekct\
|- |- |- |- |- UF_23593-24550_HF_predict_CTP-2D-02a_.info\
|- |- |- |- |- UF_23593-24550_HF_predict_CTP-2D-02a_0000.tif\
|- |- |- |- |- UF_23593-24550_HF_predict_CTP-2D-02a_XXXX.tif\
|- |- |- |- |- UF_23593-24550_HF_predict_CTP-2D-02a_1663.tif\
|- |- |- |- Predict_CTP-3D-02a\
|- |- |- |- |- _UF_23593-24550_HF.xtekct\
|- |- |- |- |- UF_23593-24550_HF_predict_CTP-3D-02a_.info\
|- |- |- |- |- UF_23593-24550_HF_predict_CTP-3D-02a_0000.tif\
|- |- |- |- |- UF_23593-24550_HF_predict_CTP-3D-02a_XXXX.tif\
|- |- |- |- |- UF_23593-24550_HF_predict_CTP-3D-02a_1663.tif
UF_24550_TFiRU.zip\
|- Data\
|- |- Fitting\
|- |- |- UF_24550_TFiRU\
|- |- |- |- _Raw\
|- |- |- |- |- _UF_24550_TFiRU.xtekct\
|- |- |- |- |- UF_24550_TFiRU_.info\
|- |- |- |- |- UF_24550_TFiRU_0000.tif\
|- |- |- |- |- UF_24550_TFiRU_XXXX.tif\
|- |- |- |- |- UF_24550_TFiRU_2047.tif\
|- |- |- |- CTP-label\
|- |- |- |- |- _UF_24550_TFiRU.xtekct\
|- |- |- |- |- UF_24550_TFiRU_cort-trab-pores-label_v2_.info\
|- |- |- |- |- UF_24550_TFiRU_cort-trab-pores-label_v2_0000.tif\
|- |- |- |- |- UF_24550_TFiRU_cort-trab-pores-label_v2_XXXX.tif\
|- |- |- |- |- UF_24550_TFiRU_cort-trab-pores-label_v2_2047.tif\
|- |- |- |- Predict_BP-2D-02a\
|- |- |- |- |- _UF_24550_TFiRU.xtekct\
|- |- |- |- |- UF_24550_TFiRU_predict_BP-2D-02a_.info\
|- |- |- |- |- UF_24550_TFiRU_predict_BP-2D-02a_0000.tif\
|- |- |- |- |- UF_24550_TFiRU_predict_BP-2D-02a_XXXX.tif\
|- |- |- |- |- UF_24550_TFiRU_predict_BP-2D-02a_2047.tif\
|- |- |- |- Predict_BP-3D-02a\
|- |- |- |- |- _UF_24550_TFiRU.xtekct\
|- |- |- |- |- UF_24550_TFiRU_predict_BP-3D-02a_.info\
|- |- |- |- |- UF_24550_TFiRU_predict_BP-3D-02a_0000.tif\
|- |- |- |- |- UF_24550_TFiRU_predict_BP-3D-02a_XXXX.tif\
|- |- |- |- |- UF_24550_TFiRU_predict_BP-3D-02a_2047.tif\
|- |- |- |- Predict_CTP-2D-02a\
|- |- |- |- |- _UF_24550_TFiRU.xtekct\
|- |- |- |- |- UF_24550_TFiRU_predict_CTP-2D-02a_.info\
|- |- |- |- |- UF_24550_TFiRU_predict_CTP-2D-02a_0000.tif\
|- |- |- |- |- UF_24550_TFiRU_predict_CTP-2D-02a_XXXX.tif\
|- |- |- |- |- UF_24550_TFiRU_predict_CTP-2D-02a_2047.tif\
|- |- |- |- Predict_CTP-3D-02a\
|- |- |- |- |- _UF_24550_TFiRU.xtekct\
|- |- |- |- |- UF_24550_TFiRU_predict_CTP-3D-02a_.info\
|- |- |- |- |- UF_24550_TFiRU_predict_CTP-3D-02a_0000.tif\
|- |- |- |- |- UF_24550_TFiRU_predict_CTP-3D-02a_XXXX.tif\
|- |- |- |- |- UF_24550_TFiRU_predict_CTP-3D-02a_2047.tif
UF_31151_HRU.zip\
|- Data\
|- |- Fitting\
|- |- |- UF_31151_HRU\
|- |- |- |- _Raw\
|- |- |- |- |- _UF_31151_HRU.xtekct\
|- |- |- |- |- UF_31151_HRU_.info\
|- |- |- |- |- UF_31151_HRU_0000.tif\
|- |- |- |- |- UF_31151_HRU_XXXX.tif\
|- |- |- |- |- UF_31151_HRU_1663.tif\
|- |- |- |- CTP-label\
|- |- |- |- |- _UF_31151_HRU.xtekct\
|- |- |- |- |- UF_31151_HRU_cort-trab-pores-label_v2_.info\
|- |- |- |- |- UF_31151_HRU_cort-trab-pores-label_v2_0000.tif\
|- |- |- |- |- UF_31151_HRU_cort-trab-pores-label_v2_XXXX.tif\
|- |- |- |- |- UF_31151_HRU_cort-trab-pores-label_v2_1663.tif\
|- |- |- |- Predict_BP-2D-02a\
|- |- |- |- |- _UF_31151_HRU.xtekct\
|- |- |- |- |- UF_31151_HRU_predict_BP-2D-02a_.info\
|- |- |- |- |- UF_31151_HRU_predict_BP-2D-02a_0000.tif\
|- |- |- |- |- UF_31151_HRU_predict_BP-2D-02a_XXXX.tif\
|- |- |- |- |- UF_31151_HRU_predict_BP-2D-02a_1663.tif\
|- |- |- |- Predict_BP-3D-02a\
|- |- |- |- |- _UF_31151_HRU.xtekct\
|- |- |- |- |- UF_31151_HRU_predict_BP-3D-02a_.info\
|- |- |- |- |- UF_31151_HRU_predict_BP-3D-02a_0000.tif\
|- |- |- |- |- UF_31151_HRU_predict_BP-3D-02a_XXXX.tif\
|- |- |- |- |- UF_31151_HRU_predict_BP-3D-02a_1663.tif\
|- |- |- |- Predict_CTP-2D-02a\
|- |- |- |- |- _UF_31151_HRU.xtekct\
|- |- |- |- |- UF_31151_HRU_predict_CTP-2D-02a_.info\
|- |- |- |- |- UF_31151_HRU_predict_CTP-2D-02a_0000.tif\
|- |- |- |- |- UF_31151_HRU_predict_CTP-2D-02a_XXXX.tif\
|- |- |- |- |- UF_31151_HRU_predict_CTP-2D-02a_1663.tif\
|- |- |- |- Predict_CTP-3D-02a\
|- |- |- |- |- _UF_31151_HRU.xtekct\
|- |- |- |- |- UF_31151_HRU_predict_CTP-3D-02a_.info\
|- |- |- |- |- UF_31151_HRU_predict_CTP-3D-02a_0000.tif\
|- |- |- |- |- UF_31151_HRU_predict_CTP-3D-02a_XXXX.tif\
|- |- |- |- |- UF_31151_HRU_predict_CTP-3D-02a_1663.tif
Sharing/Access information
Free sharing of data, models, and code under CC0 1.0. Please cite accompanying paper if materials are used in part or whole for other applications.
Code/Software
n/a
Methods
Materials
Limb bones from the North American river otter (Lontra canadensis) were borrowed from four museums — OMNH (SNM): Sam Noble Oklahoma Museum of Natural History (Norman Oklahoma); UAM: University of Alaska Museum of the North (Fairbanks, Alaska); and UF: Florida Museum of Natural History (Gainesville, Florida); UWBM (BM): Burke Museum of Natural History and Culture (Seattle, Washington). In total, the sample consisted of 38 elements (humerus, radius, ulna, femur, tibia, and fibula) from nine individuals.
Specimen |
kV |
µA |
Filter |
Res. (µm) |
Provenance |
Sex |
Side |
Element |
Group |
OMNH 44262 |
160 |
312 |
Copper |
49.99 |
Tennessee |
F |
R |
Humerus |
Fitting |
|
|
|
|
|
|
|
L |
Radius |
Fitting |
|
|
|
|
|
|
|
L |
Ulna |
Fitting |
OMNH 53994 |
160 |
312 |
Copper |
49.99 |
Tennessee |
M |
L |
Femur |
Fitting |
|
|
|
|
|
|
|
L |
Fibula |
Fitting |
|
|
|
|
|
|
|
L |
Humerus |
Testing |
|
|
|
|
|
|
|
R |
Radius |
Testing |
|
|
|
|
|
|
|
L |
Tibia |
Fitting |
|
|
|
|
|
|
|
R |
Ulna |
Testing |
UAM 24789 |
160 |
312 |
Copper |
49.99 |
Alaska |
M |
R |
Femur |
Testing |
|
|
|
|
|
|
|
R |
Fibula |
Testing |
|
|
|
|
|
|
|
R |
Tibia |
Testing |
UAM 67696 |
90 |
556 |
None |
49.99 |
Alaska |
F |
L |
Femur |
Fitting |
|
|
|
|
|
|
|
L |
Humerus |
Fitting |
|
160 |
312 |
Copper |
49.99 |
|
|
L |
Fibula |
Fitting |
|
160 |
312 |
Copper |
|
|
|
L |
Radius |
Fitting |
|
160 |
312 |
Copper |
|
|
|
L |
Tibia |
Fitting |
|
160 |
312 |
Copper |
|
|
|
L |
Ulna |
Fitting |
UF 23593 |
79 |
633 |
None |
49.99 |
Florida |
M |
L |
Femur |
Fitting |
|
|
|
|
|
|
|
L |
Humerus |
Fitting |
UF 24550 |
79 |
633 |
None |
49.99 |
Florida |
F |
L |
Femur |
Fitting |
|
|
|
|
|
|
|
L |
Humerus |
Fitting |
|
160 |
312 |
Copper |
49.99 |
|
|
L |
Fibula |
Fitting |
|
|
|
|
|
|
|
L |
Radius |
Fitting |
|
|
|
|
|
|
|
L |
Tibia |
Fitting |
|
|
|
|
|
|
|
L |
Ulna |
Fitting |
UF 31151 |
160 |
312 |
Copper |
49.99 |
Florida |
M |
R |
Humerus |
Fitting |
|
|
|
|
|
|
|
R |
Radius |
Fitting |
|
|
|
|
|
|
|
R |
Ulna |
Fitting |
UWBM 78743 |
160 |
312 |
Copper |
49.99 |
Washington |
F |
R |
Femur |
Fitting |
|
|
|
|
|
|
|
L |
Fibula |
Fitting |
|
|
|
|
|
|
|
L |
Tibia |
Fitting |
UWBM 81969 |
160 |
312 |
Copper |
49.99 |
Washington |
M |
R |
Femur |
Testing |
|
|
|
|
|
|
|
L |
Fibula |
Testing |
|
|
|
|
|
|
|
L |
Humerus |
Testing |
|
|
|
|
|
|
|
R |
Radius |
Testing |
|
|
|
|
|
|
|
L |
Tibia |
Testing |
|
|
|
|
|
|
|
R |
Ulna |
Testing |
Imaging
Bones were scanned at the University of Arkansas MICRO lab using a Nikon XTH 225 ST. Scans were performed in sets of 2-4 bones. Scan settings are included in the preceding table. Of the 12 sets, eight were used for training/validation and four were reserved for blind testing.
Reference segmentation
Reference segmentations were prepared using Avizo 3D 2024.1 (Thermo Fisher Scientific, Waltham, MA, USA). The 16-bit grayscale contrast of each volume was improved using the “Sigmoid Intensity Remapping” operation set to 3D mode. Bone tissue was initially segmented using the “Auto Thresholding” module (default settings) and manually inspected for mislabeling. Trabecular bone that was missed by auto thresholding was added to the bone tissue segmentation using the “Top Hat” filter. Medullary spaces and large vascular canals (hereafter referred to as “pores”) were isolated using the 3D ray tracing “Compute Ambient Occlusion” operation on the bone segmentation. Trabecular bone was segmented following the “shrink-wrap” approach of Herbst et al. (2021). Briefly, this approach creates a masking volume that circumscribes major pores. Bone tissue within this mask volume is classified as trabecular bone, whereas bone tissue outside the volume is classified as cortical bone. Image preparation culminated in two sets of reference data for each volume: the first with labels for bone tissue and pores (BP); and the second with labels for cortical bone, trabecular bone, and pores (CTP).
Fitting the deep learning models
Several deep learning models were fitted using Avizo 3D with TensorFlow (Google, Mountain View, California) as the backend. The architecture of each model was pre-built consisting of a U-Net convolutional neural network with a ResNet-18 encoder. We fitted models separately on 2D (e.g., single slice) and 3D (e.g., volumetric) data. We also fitted models to segment bone and medullary pores separately from those to segment cortical bone, trabecular bone, and medullary pores. Each model was pre-trained on UWBM 78743 and subsequently fine-tuned on a larger composite dataset containing several specimens. Note: a pre-trained model represents an intermediate stage in fitting that we share for data transparency. The fine-tuned model is finalized and ready for general use.
List of 2D models
Abbreviations: B = bone; P = medullary pores; C = cortical bone; T = trabecular bone
Bold = finalized model
Name |
Training stage |
Segmentation goal |
BP-2D-02 |
Pre-train |
Bone tissue and medullary pores |
BP-2D-02a |
Fine-tune |
Bone tissue and medullary pores |
CTP-2D-02 |
Pre-train |
Cortical bone, trabecular bone, medullary pores |
CTP-2D-02a |
Fine-tune |
Cortical bone, trabecular bone, medullary pores |
List of 3D models
Abbreviations: B = bone; P = medullary pores; C = cortical bone; T = trabecular bone
Bold = finalized model
Name |
Training stage |
Segmentation goal |
BP-3D-02 |
Pre-train |
Bone tissue and medullary pores |
BP-3D-02a |
Fine-tune |
Bone tissue and medullary pores |
CTP-3D-02 |
Pre-train |
Cortical bone, trabecular bone, medullary pores |
CTP-3D-02a |
Fine-tune |
Cortical bone, trabecular bone, medullary pores |