biomedisa 24.7.1

Segmentation of 3D volumetric image data

• Overview
• Hardware Requirements
• Installation (command-line based)
• Installation (browser based)
• Download Data
• Revisions
• Quickstart
• Smart Interpolation
• Deep Learning
• Mesh Generator
• Biomedisa Features
• Authors
• FAQ
• Citation
• License

Overview

Biomedisa (https://biomedisa.info) is a free and easy-to-use open-source application for segmenting large 3D volumetric images such as CT and MRI scans, developed at The Australian National University CTLab. Biomedisa's smart interpolation of sparsely pre-segmented slices enables accurate semi-automated segmentation by considering the complete underlying image data. Additionally, Biomedisa enables deep learning for fully automated segmentation across similar samples and structures. It is compatible with segmentation tools like Amira/Avizo, ImageJ/Fiji and 3D Slicer. If you are using Biomedisa or the data for your research please cite: Lösel, P.D. et al. Introducing Biomedisa as an open-source online platform for biomedical image segmentation. Nat. Commun. 11, 5577 (2020).

Hardware Requirements

• One or more NVIDIA GPUs with compute capability 3.0 or higher or an Intel CPU

Installation (command-line based)

• Ubuntu 22.04 + CUDA + GPU (recommended)
• Ubuntu 22.04 + OpenCL + CPU (very slow)
• Windows 10 + CUDA + GPU (recommended)
• Windows 10 + OpenCL + GPU (easy to install but lacks features like allaxis, smoothing, uncertainty, optimized GPU memory usage)
• Windows 10 + OpenCL + CPU (very slow)

Installation (3D Slicer extension)

• Ubuntu 22.04 + CUDA + GPU

Installation (browser based)

• Ubuntu 22.04

Download Data

• Download test data from our gallery

Revisions

24.7.1

• 3D Slicer extension
• Prediction of large data block by block 24.5.22
• Pip is the preferred installation method
• Commands, module names and imports have been changed to conform to the Pip standard
• For versions <=23.9.1 please check README

Quickstart

Install the Biomedisa package from the Python Package Index:

python -m pip install -U biomedisa

For smart interpolation and deep Learning modules, follow the installation instructions above.

Smart Interpolation

• Parameters and Examples

Python example

from biomedisa.features.biomedisa_helper import load_data, save_data
from biomedisa.interpolation import smart_interpolation

# load data
img, _ = load_data('Downloads/trigonopterus.tif')
labels, header = load_data('Downloads/labels.trigonopterus_smart.am')

# run smart interpolation with optional smoothing result
results = smart_interpolation(img, labels, smooth=100)

# get results
regular_result = results['regular']
smooth_result = results['smooth']

# save results
save_data('Downloads/final.trigonopterus.am', regular_result, header=header)
save_data('Downloads/final.trigonopterus.smooth.am', smooth_result, header=header)

Command-line based

python -m biomedisa.interpolation C:\Users\%USERNAME%\Downloads\tumor.tif C:\Users\%USERNAME%\Downloads\labels.tumor.tif

If pre-segmentation is not exclusively in the XY plane:

python -m biomedisa.interpolation C:\Users\%USERNAME%\Downloads\tumor.tif C:\Users\%USERNAME%\Downloads\labels.tumor.tif --allaxis

Deep Learning

• Parameters and Examples

Python example (training)

from biomedisa.features.biomedisa_helper import load_data
from biomedisa.deeplearning import deep_learning

# load image data
img1, _ = load_data('Head1.am')
img2, _ = load_data('Head2.am')
img_data = [img1, img2]

# load label data and header information to be stored in the network file (optional)
label1, _ = load_data('Head1.labels.am')
label2, header, ext = load_data('Head2.labels.am',
        return_extension=True)
label_data = [label1, label2]

# load validation data (optional)
img3, _ = load_data('Head3.am')
img4, _ = load_data('Head4.am')
label3, _ = load_data('Head3.labels.am')
label4, _ = load_data('Head4.labels.am')
val_img_data = [img3, img4]
val_label_data = [label3, label4]

# deep learning 
deep_learning(img_data, label_data, train=True, batch_size=12,
        val_img_data=val_img_data, val_label_data=val_label_data,
        header=header, extension=ext, path_to_model='honeybees.h5')

Command-line based (training)

python -m biomedisa.deeplearning C:\Users\%USERNAME%\Downloads\training_heart C:\Users\%USERNAME%\Downloads\training_heart_labels -t

Monitor training progress using validation data:

python -m biomedisa.deeplearning C:\Users\%USERNAME%\Downloads\training_heart C:\Users\%USERNAME%\Downloads\training_heart_labels -t -vi=C:\Users\%USERNAME%\Downloads\val_img -vl=C:\Users\%USERNAME%\Downloads\val_labels

If running into ResourceExhaustedError due to out of memory (OOM), try to use a smaller batch size (e.g. -bs=12).

Python example (prediction)

from biomedisa.features.biomedisa_helper import load_data, save_data
from biomedisa.deeplearning import deep_learning

# load data
img, _ = load_data('Head5.am')

# deep learning
results = deep_learning(img, predict=True,
        path_to_model='honeybees.h5', batch_size=6)

# save result
save_data('final.Head5.am', results['regular'], results['header'])

Command-line based (prediction)

python -m biomedisa.deeplearning C:\Users\%USERNAME%\Downloads\testing_axial_crop_pat13.nii.gz C:\Users\%USERNAME%\Downloads\heart.h5 -p

Mesh Generator

• Parameters and Examples

Python example

Create STL mesh from segmentation (label values are saved as attributes)

from biomedisa.features.biomedisa_helper import load_data, save_data
from biomedisa.mesh import get_voxel_spacing, save_mesh

# load segmentation
data, header, extension = load_data('final.Head5.am', return_extension=True)

# get voxel spacing
x_res, y_res, z_res = get_voxel_spacing(header, extension)
print(f'Voxel spacing: x_spacing, y_spacing, z_spacing = {x_res}, {y_res}, {z_res}')

# save stl file
save_mesh('final.Head5.stl', data, x_res, y_res, z_res, poly_reduction=0.9, smoothing_iterations=15)

Command-line based

python -m biomedisa.mesh 'final.Head5.am'

Biomedisa Features

Load and save data (such as Amira Mesh, TIFF, NRRD, NIfTI or DICOM)

For DICOM, PNG files, or similar formats, file path must reference either a directory or a ZIP file containing the image slices.

from biomedisa.features.biomedisa_helper import load_data, save_data

# load data as numpy array
data, header = load_data('temp.tif')

# save data (for TIFF, header=None)
save_data('temp.tif', data, header)

Resize data

from biomedisa.features.biomedisa_helper import img_resize

# resize image data
zsh, ysh, xsh = data.shape
new_zsh, new_ysh, new_xsh = zsh//2, ysh//2, xsh//2
data = img_resize(data, new_zsh, new_ysh, new_xsh)

# resize label data
label_data = img_resize(label_data, new_zsh, new_ysh, new_xsh, labels=True)

Remove outliers and fill holes

from biomedisa.features.biomedisa_helper import clean, fill

# delete outliers smaller than 90% of the segment
label_data = clean(label_data, 0.9)

# fill holes
label_data = fill(label_data, 0.9)

Accuracy assessment

from biomedisa.features.biomedisa_helper import Dice_score, ASSD
dice = Dice_score(ground_truth, result)
assd = ASSD(ground_truth, result)

Authors

• Philipp D. Lösel

See also the list of contributors who participated in this project.

FAQ

Frequently asked questions can be found at: https://biomedisa.info/faq/.

Citation

If you use Biomedisa or the data, please cite the following paper:

Lösel, P.D. et al. Introducing Biomedisa as an open-source online platform for biomedical image segmentation. Nat. Commun. 11, 5577 (2020). https://doi.org/10.1038/s41467-020-19303-w

If you use Biomedisa's Deep Learning, you may also cite:

Lösel, P.D. et al. Natural variability in bee brain size and symmetry revealed by micro-CT imaging and deep learning. PLoS Comput. Biol. 19, e1011529 (2023). https://doi.org/10.1371/journal.pcbi.1011529

If you use Biomedisa's Smart Interpolation, you can also cite the initial description of this method:

Lösel, P. & Heuveline, V. Enhancing a diffusion algorithm for 4D image segmentation using local information. Proc. SPIE 9784, 97842L (2016). https://doi.org/10.1117/12.2216202

License

This project is covered under the EUROPEAN UNION PUBLIC LICENCE v. 1.2 (EUPL).