biomedisa 2024.5.14__tar.gz

biomedisa-2024.5.14/LICENSE

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biomedisa-2024.5.14/PKG-INFO

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+Metadata-Version: 2.1
+Name: biomedisa
+Version: 2024.5.14
+Summary: Segmentation of 3D volumetric image data
+Author: Philipp Lösel
+Author-email: philipp.loesel@anu.edu.au
+Project-URL: Homepage, https://biomedisa.info
+Project-URL: Issues, https://github.com/biomedisa/biomedisa/issues
+Project-URL: GitHub, https://github.com/biomedisa/biomedisa
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: European Union Public Licence 1.2 (EUPL 1.2)
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+[![biomedisa](biomedisa_app/static/biomedisa_logo.svg)](https://biomedisa.info)
+-----------
+- [Overview](#overview)
+- [Hardware Requirements](#hardware-requirements)
+- [Installation (command-line based)](#installation-command-line-based)
+- [Installation (browser based)](#installation-browser-based)
+- [Download Data](#download-data)
+- [Smart Interpolation](#smart-interpolation)
+- [Deep Learning](#deep-learning)
+- [Biomedisa Features](#biomedisa-features)
+- [Update Biomedisa](#update-biomedisa)
+- [Releases](#releases)
+- [Authors](#authors)
+- [FAQ](#faq)
+- [Citation](#citation)
+- [License](#license)
+
+# Overview
+Biomedisa (https://biomedisa.info) is a free and easy-to-use open-source application for segmenting large volumetric images, e.g. CT and MRI scans, developed at [The Australian National University CTLab](https://ctlab.anu.edu.au/). Biomedisa's semi-automated segmentation is based on a smart interpolation of sparsely pre-segmented slices, taking into account the complete underlying image data. In addition, Biomedisa enables deep learning for the fully automated segmentation of series of similar samples. It can be used in combination with segmentation tools such as 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.](https://www.nature.com/articles/s41467-020-19303-w) *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)](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu2204_cuda11.8_gpu_cli.md)
++ [Ubuntu 22.04 + OpenCL + CPU (smart interpolation only and very slow)](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu2204_opencl_cpu_cli.md)
++ [Windows 10 + CUDA + GPU (recommended)](https://github.com/biomedisa/biomedisa/blob/master/README/windows10_cuda_gpu_cli.md)
++ [Windows 10 + OpenCL + GPU (easy to install but lacks features like allaxis, smoothing, uncertainty, optimized GPU memory usage)](https://github.com/biomedisa/biomedisa/blob/master/README/windows10_opencl_gpu_cli.md)
++ [Windows 10 + OpenCL + CPU (very slow)](https://github.com/biomedisa/biomedisa/blob/master/README/windows10_opencl_cpu_cli.md)
+
+# Installation (browser based)
++ [Ubuntu 22.04](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu2204_cuda11.8.md)
+
+# Download Data
++ Download the data from our [gallery](https://biomedisa.info/gallery/)
+
+# Smart Interpolation
++ [Parameters and Examples](https://github.com/biomedisa/biomedisa/blob/master/README/smart_interpolation.md)
+
+#### Python example
+```python
+# change this line to your biomedisa directory
+path_to_biomedisa = '/home/<user>/git/biomedisa'
+
+import sys
+sys.path.append(path_to_biomedisa)
+from biomedisa_features.biomedisa_helper import load_data, save_data
+from biomedisa_features.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
+```
+# change to the features directory
+cd git/biomedisa/biomedisa_features/
+
+# start smart interpolation
+python biomedisa_interpolation.py C:\Users\%USERNAME%\Downloads\tumor.tif C:\Users\%USERNAME%\Downloads\labels.tumor.tif
+```
+
+# Deep Learning
++ [Parameters and Examples](https://github.com/biomedisa/biomedisa/blob/master/README/deep_learning.md)
+
+#### Python example (training)
+```python
+# change this line to your biomedisa directory
+path_to_biomedisa = '/home/<user>/git/biomedisa'
+
+# load libraries
+import sys
+sys.path.append(path_to_biomedisa)
+from biomedisa_features.biomedisa_helper import load_data
+from biomedisa_features.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)
+```
+# change to the features directory
+cd git/biomedisa/biomedisa_features/
+
+# start training with a batch size of 12
+python biomedisa_deeplearning.py C:\Users\%USERNAME%\Downloads\training_heart C:\Users\%USERNAME%\Downloads\training_heart_labels -t -bs 12
+
+# validation (optional)
+python biomedisa_deeplearning.py 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 smaller batch size.
+
+#### Python example (prediction)
+```python
+# change this line to your biomedisa directory
+path_to_biomedisa = '/home/<user>/git/biomedisa'
+
+# load libraries
+import sys
+sys.path.append(path_to_biomedisa)
+from biomedisa_features.biomedisa_helper import load_data, save_data
+from biomedisa_features.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)
+```
+# change to the features directory
+cd git/biomedisa/biomedisa_features/
+
+# start prediction with a batch size of 6
+python biomedisa_deeplearning.py C:\Users\%USERNAME%\Downloads\testing_axial_crop_pat13.nii.gz C:\Users\%USERNAME%\Downloads\heart.h5 -p -bs 6
+```
+
+# Biomedisa Features
+
+#### Load and save data (such as Amira Mesh, TIFF, NRRD, NIfTI or DICOM)
+```python
+import sys
+sys.path.append(path_to_biomedisa)  # e.g. '/home/<user>/git/biomedisa'
+from biomedisa_features.biomedisa_helper import load_data, save_data
+
+# load data as numpy array
+# for DICOM, PNG files, or similar formats, 'path_to_data' must reference
+# either a directory or a ZIP file containing the image slices
+data, header = load_data(path_to_data)
+
+# save data (for TIFF, header=None)
+save_data(path_to_data, data, header)
+```
+
+#### Create STL mesh from segmentation (label values are saved as attributes)
+```python
+import os, sys
+sys.path.append(path_to_biomedisa)  # e.g. '/home/<user>/git/biomedisa'
+from biomedisa_features.biomedisa_helper import load_data, save_data
+from biomedisa_features.create_mesh import get_voxel_spacing, save_mesh
+
+# load segmentation
+data, header, extension = load_data(path_to_data, return_extension=True)
+
+# get voxel spacing
+x_res, y_res, z_res = get_voxel_spacing(header, data, extension)
+print(f'Voxel spacing: x_spacing, y_spacing, z_spacing = {x_res}, {y_res}, {z_res}')
+
+# save stl file
+path_to_data = path_to_data.replace(os.path.splitext(path_to_data)[1],'.stl')
+save_mesh(path_to_data, data, x_res, y_res, z_res, poly_reduction=0.9, smoothing_iterations=15)
+```
+
+#### Create mesh directly
+```
+python git/biomedisa/biomedisa_features/create_mesh.py <path_to_data>
+```
+
+#### Options
+`--poly_reduction` or `-pr`: Reduce number of polygons by this factor (default: 0.9)
+
+`--smoothing_iterations` or `-s`: Iteration steps for smoothing (default: 15)
+
+`--x_res` or `-xres`: Voxel spacing/resolution x-axis (default: None)
+
+`--y_res` or `-yres`: Voxel spacing/resolution y-axis (default: None)
+
+`--z_res` or `-zres`: Voxel spacing/resolution z-axis (default: None)
+
+#### Resize data
+```python
+import os, sys
+sys.path.append(path_to_biomedisa)  # e.g. '/home/<user>/git/biomedisa'
+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
+```python
+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
+```python
+from biomedisa_features.biomedisa_helper import Dice_score, ASSD
+dice = Dice_score(ground_truth, result)
+assd = ASSD(ground_truth, result)
+```
+
+# Update Biomedisa
+If you have used `git clone`, change to the Biomedisa directory and make a pull request.
+```
+cd git/biomedisa
+git pull
+```
+
+If you have installed the browser based version of Biomedisa (including MySQL database), you also need to update the database.
+```
+python manage.py migrate
+```
+
+If you have installed an [Apache Server](https://github.com/biomedisa/biomedisa/blob/master/README/APACHE_SERVER.md), you need to restart the server.
+```
+sudo service apache2 restart
+```
+
+# Releases
+
+For the versions available, see the [list of releases](https://github.com/biomedisa/biomedisa/releases). 
+
+# Authors
+
+* **Philipp D. Lösel**
+
+See also the list of [contributors](https://github.com/biomedisa/biomedisa/blob/master/credits.md) 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)**.
+