cropro 0.1.2__tar.gz

cropro-0.1.2/LICENSE

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+MIT License
+
+Copyright (c) 2023 Alexandros Patsanis
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

cropro-0.1.2/PKG-INFO

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+Metadata-Version: 2.4
+Name: cropro
+Version: 0.1.2
+Summary: Automated cropping of prostate MR images.
+Author: Alexandors Patsanis
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/alexofficial/CROPro
+Project-URL: Repository, https://github.com/alexofficial/CROPro
+Project-URL: Issues, https://github.com/alexofficial/CROPro/issues
+Keywords: medical-imaging,mri,prostate,cropping,picai
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.13
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: matplotlib>=3.10.9
+Requires-Dist: numpy>=2.4.6
+Requires-Dist: opencv-python>=4.13.0.92
+Requires-Dist: SimpleITK>=2.5.5
+Provides-Extra: dev
+Requires-Dist: bandit>=1.7; extra == "dev"
+Requires-Dist: build>=1; extra == "dev"
+Requires-Dist: pip-audit>=2.7; extra == "dev"
+Requires-Dist: pytest>=8; extra == "dev"
+Requires-Dist: ruff>=0.5; extra == "dev"
+Requires-Dist: twine>=5; extra == "dev"
+Dynamic: license-file
+
+# CROPro
+
+CROPro is a Python package for automated cropping of prostate MRI volumes. It was developed for prostate MR preprocessing workflows where a model or reviewer needs consistent image patches around the prostate gland or clinically significant prostate cancer lesions.
+
+The package supports:
+
+- `center`, `random`, and `stride` crop strategies
+- T2W-only and bpMRI cropping workflows
+- negative, positive, and unknown patient-status workflows
+- configurable in-plane resampling through `pixel_spacing`
+- Python API and command-line usage
+
+If you use CROPro in research, please cite the paper listed in [Citation](#citation):
+`CROPro: a tool for automated cropping of prostate magnetic resonance images`.
+
+## Contents
+
+- [Installation](#installation)
+- [Quick Start](#quick-start)
+- [Input Data](#input-data)
+- [Patient Workflows](#patient-workflows)
+- [Visual Examples](#visual-examples)
+- [Pixel Spacing](#pixel-spacing)
+- [PI-CAI Dataset Setup](#pi-cai-dataset-setup)
+- [Command Line](#command-line)
+- [Configuration Reference](#configuration-reference)
+- [Development](#development)
+- [PyPI Release](#pypi-release)
+- [Citation](#citation)
+
+## Installation
+
+This repository uses [`uv`](https://docs.astral.sh/uv/) for dependency management.
+
+Install `uv` if needed:
+
+```bash
+curl -LsSf https://astral.sh/uv/install.sh | sh
+```
+
+Clone the repository and install the environment:
+
+```bash
+git clone https://github.com/alexofficial/CROPro.git
+cd CROPro
+uv sync
+```
+
+Check that the CLI is available:
+
+```bash
+uv run cropro --help
+```
+
+For development tools such as tests and linting:
+
+```bash
+uv sync --extra dev
+```
+
+When CROPro is published to PyPI, users will be able to install it in a project with:
+
+```bash
+uv add cropro
+```
+
+For CLI-only use after PyPI publication:
+
+```bash
+uv tool install cropro
+cropro --help
+```
+
+## PyPI Release
+
+This repository is configured to publish to PyPI through GitHub Actions using Trusted Publishing.
+
+### One-Time Setup
+
+1. On PyPI, create a project named `cropro` (or claim it if it already exists under your account).
+2. In PyPI project settings, configure a Trusted Publisher for this GitHub repository and workflow:
+  - owner/repo: `alexofficial/CROPro`
+  - workflow filename: `.github/workflows/pypi-publish.yml`
+  - environment: `pypi`
+
+### Release Flow
+
+1. Update version in `pyproject.toml`.
+2. Commit and push to `main`.
+3. Create a GitHub release (for example tag `v0.1.1`).
+4. The `Publish to PyPI` workflow builds the package and uploads it to PyPI.
+
+### Optional Local Validation
+
+```bash
+python -m build
+python -m twine check dist/*
+```
+
+## Quick Start
+
+### Crop A Negative Or Unknown Case
+
+Use this when you have a T2W image and a prostate gland mask. For `unknown` patient status, CROPro uses the same gland-mask workflow as `negative`, which is useful for inference or review cases where cancer status is not known yet.
+
+```python
+from cropro import CROPro, CropConfig
+
+config = CropConfig(
+    crop_method="stride",
+    patient_status="negative",  # "negative" or "unknown"
+    sequence_type="T2W",
+    orig_img_path_t2w="data/patient_001/t2w.nii.gz",
+    seg_img_path="data/patient_001/prostate_gland_mask.nii.gz",
+    pixel_spacing=0.4,
+    crop_image_size=128,
+    crop_stride=32,
+    saved_image_type="png",
+    path_to_save="outputs/patient_001",
+)
+
+CROPro(config).run()
+```
+
+### Crop A Positive Case
+
+Use this when you have a prostate gland mask and a lesion mask. The gland mask defines the anatomical search region; the lesion mask is used to keep crops that contain enough lesion area.
+
+```python
+from cropro import CROPro, CropConfig
+
+config = CropConfig(
+    crop_method="stride",
+    patient_status="positive",
+    sequence_type="T2W",
+    orig_img_path_t2w="data/patient_002/t2w.nii.gz",
+    seg_img_path="data/patient_002/prostate_gland_mask.nii.gz",
+    seg_img_path_lesion="data/patient_002/lesion_mask.nii.gz",
+    tumor_label_level=1,
+    c_min_positive=0.2,
+    pixel_spacing=0.4,
+    crop_image_size=128,
+    crop_stride=32,
+    saved_image_type="png",
+    path_to_save="outputs/patient_002",
+)
+
+CROPro(config).run()
+```
+
+### Crop bpMRI
+
+Set `sequence_type="bpMRI"` and provide T2W, ADC, and HBV images. CROPro saves aligned crops for each modality.
+
+```python
+from cropro import CROPro, CropConfig
+
+config = CropConfig(
+    crop_method="center",
+    patient_status="negative",
+    sequence_type="bpMRI",
+    orig_img_path_t2w="data/patient_003/t2w.nii.gz",
+    orig_img_path_adc="data/patient_003/adc.nii.gz",
+    orig_img_path_hbv="data/patient_003/hbv.nii.gz",
+    seg_img_path="data/patient_003/prostate_gland_mask.nii.gz",
+    pixel_spacing=0.5,
+    crop_image_size=128,
+    saved_image_type="png",
+    path_to_save="outputs/patient_003",
+)
+
+CROPro(config).run()
+```
+
+## Input Data
+
+CROPro reads 3D medical image files through SimpleITK. Common formats include `.nii`, `.nii.gz`, `.mha`, `.mhd`, and other SimpleITK-readable formats.
+
+For a negative or unknown patient, provide:
+
+- T2W image
+- prostate gland segmentation mask
+
+For a positive patient, provide:
+
+- T2W image
+- prostate gland segmentation mask
+- lesion segmentation mask
+
+For `sequence_type="bpMRI"`, also provide:
+
+- ADC image
+- HBV image
+
+All images and masks should already be spatially aligned. CROPro resamples the image spacing for crop generation, but it does not perform image registration.
+
+## Patient Workflows
+
+| Status | Intended use | Segmentation behavior |
+| --- | --- | --- |
+| `negative` | Cancer-free cases | Uses the prostate gland mask to crop the prostate region. |
+| `positive` | Cancer-present cases | Uses the prostate gland mask for crop placement and the lesion mask to keep crops containing enough lesion area. |
+| `unknown` | Inference, testing, or review cases with unknown health status | Uses the prostate gland mask like the negative workflow and returns candidate prostate-region crops. |
+
+## Visual Examples
+
+### Negative Or Unknown Workflow
+
+For negative and unknown cases, the prostate gland mask defines the region to crop.
+
+<p>
+  <img src="./assets/readme/segmentation/negative/PICAI/10001_1000001/T2W/T2W_axial0007.png" width="220" alt="T2W prostate gland segmentation example" />
+  <img src="./assets/readme/segmentation/negative/PICAI/10001_1000001/ADC/ADC_axial0007.png" width="220" alt="ADC prostate gland segmentation example" />
+  <img src="./assets/readme/segmentation/negative/PICAI/10001_1000001/HBV/HBV_axial0007.png" width="220" alt="HBV prostate gland segmentation example" />
+</p>
+
+Stride-cropped bpMRI output at `0.4` mm/pixel. With `crop_image_size=128`, the crop covers about `51.2 x 51.2` mm.
+
+<p>
+  <img src="./assets/readme/negative/PICAI_stride_0.4_128_negative/10001_1000001/bpMRI_slice_7_of_21_1_cord_160_166_T2W.png" width="128" alt="Negative T2W crop at 0.4 mm pixel spacing" />
+  <img src="./assets/readme/negative/PICAI_stride_0.4_128_negative/10001_1000001/bpMRI_slice_7_of_21_1_cord_160_166_ADC.png" width="128" alt="Negative ADC crop at 0.4 mm pixel spacing" />
+  <img src="./assets/readme/negative/PICAI_stride_0.4_128_negative/10001_1000001/bpMRI_slice_7_of_21_1_cord_160_166_HBV.png" width="128" alt="Negative HBV crop at 0.4 mm pixel spacing" />
+</p>
+
+The same case at `0.5` mm/pixel covers about `64.0 x 64.0` mm and includes more surrounding context.
+
+<p>
+  <img src="./assets/readme/negative/PICAI_stride_0.5_128_negative/10001_1000001/bpMRI_slice_7_of_21_1_cord_128_132_T2W.png" width="128" alt="Negative T2W crop at 0.5 mm pixel spacing" />
+  <img src="./assets/readme/negative/PICAI_stride_0.5_128_negative/10001_1000001/bpMRI_slice_7_of_21_1_cord_128_132_ADC.png" width="128" alt="Negative ADC crop at 0.5 mm pixel spacing" />
+  <img src="./assets/readme/negative/PICAI_stride_0.5_128_negative/10001_1000001/bpMRI_slice_7_of_21_1_cord_128_132_HBV.png" width="128" alt="Negative HBV crop at 0.5 mm pixel spacing" />
+</p>
+
+### Positive Workflow
+
+For positive cases, CROPro uses the prostate gland mask plus a lesion mask. A crop is saved only when the lesion area inside the crop satisfies the configured threshold.
+
+<p>
+  <img src="./assets/readme/segmentation/positive/PICAI/10117_1000117/human/t2w-human/axial15_seg.png" width="220" alt="T2W lesion segmentation example" />
+  <img src="./assets/readme/segmentation/positive/PICAI/10117_1000117/human/adc-human/axial15_seg.png" width="220" alt="ADC lesion segmentation example" />
+  <img src="./assets/readme/segmentation/positive/PICAI/10117_1000117/human/hbv-human/axial15_seg.png" width="220" alt="HBV lesion segmentation example" />
+</p>
+
+Stride-cropped bpMRI output at `0.4` mm/pixel:
+
+<p>
+  <img src="./assets/readme/positive/PICAI_stride_0.4_128_positive/10117_1000117/bpMRI_slice_15_of_27_1_cord_157_136_T2W.png" width="128" alt="Positive T2W crop at 0.4 mm pixel spacing" />
+  <img src="./assets/readme/positive/PICAI_stride_0.4_128_positive/10117_1000117/bpMRI_slice_15_of_27_1_cord_157_136_ADC.png" width="128" alt="Positive ADC crop at 0.4 mm pixel spacing" />
+  <img src="./assets/readme/positive/PICAI_stride_0.4_128_positive/10117_1000117/bpMRI_slice_15_of_27_1_cord_157_136_HBV.png" width="128" alt="Positive HBV crop at 0.4 mm pixel spacing" />
+</p>
+
+The same positive case at `0.5` mm/pixel:
+
+<p>
+  <img src="./assets/readme/positive/PICAI_stride_0.5_128_positive/10117_1000117/bpMRI_slice_15_of_27_1_cord_126_99_T2W.png" width="128" alt="Positive T2W crop at 0.5 mm pixel spacing" />
+  <img src="./assets/readme/positive/PICAI_stride_0.5_128_positive/10117_1000117/bpMRI_slice_15_of_27_1_cord_126_99_ADC.png" width="128" alt="Positive ADC crop at 0.5 mm pixel spacing" />
+  <img src="./assets/readme/positive/PICAI_stride_0.5_128_positive/10117_1000117/bpMRI_slice_15_of_27_1_cord_126_99_HBV.png" width="128" alt="Positive HBV crop at 0.5 mm pixel spacing" />
+</p>
+
+## Pixel Spacing
+
+`pixel_spacing` controls the target in-plane resolution in millimeters per pixel before cropping. This matters because prostate MRI scans can come from different scanners, protocols, and reconstruction settings. Resampling to a consistent spacing makes crops more comparable across patients.
+
+With `crop_image_size=128`:
+
+| Pixel spacing | Crop size in pixels | Approximate physical area |
+| --- | --- | --- |
+| `0.4` mm/pixel | `128 x 128` | `51.2 x 51.2` mm |
+| `0.5` mm/pixel | `128 x 128` | `64.0 x 64.0` mm |
+
+A `0.4` mm/pixel crop is tighter around the anatomy. A `0.5` mm/pixel crop covers a wider physical region and can preserve more surrounding anatomical context.
+
+```python
+from cropro import CROPro, CropConfig
+
+tight_crop = CropConfig(
+    crop_method="center",
+    patient_status="negative",
+    sequence_type="T2W",
+    orig_img_path_t2w="data/patient_001/t2w.nii.gz",
+    seg_img_path="data/patient_001/prostate_gland_mask.nii.gz",
+    pixel_spacing=0.4,
+    crop_image_size=128,
+    path_to_save="outputs/patient_001_spacing_0.4",
+)
+
+wide_crop = CropConfig(
+    crop_method="center",
+    patient_status="negative",
+    sequence_type="T2W",
+    orig_img_path_t2w="data/patient_001/t2w.nii.gz",
+    seg_img_path="data/patient_001/prostate_gland_mask.nii.gz",
+    pixel_spacing=0.5,
+    crop_image_size=128,
+    path_to_save="outputs/patient_001_spacing_0.5",
+)
+
+CROPro(tight_crop).run()
+CROPro(wide_crop).run()
+```
+
+## PI-CAI Dataset Setup
+
+The runnable examples use the official PI-CAI Public Training and Development Dataset. Images are hosted on Zenodo, and annotations are maintained in the `DIAGNijmegen/picai_labels` repository.
+
+The default download fetches public image fold 0, which is about 5.4 GB, and clones the labels:
+
+```bash
+uv sync
+bash scripts/download_dataset.sh
+```
+
+The script writes data under `dataset/PI-CAI/`. This directory is ignored by git.
+
+The image download is resumable because the script uses `curl -C -`. If the download is interrupted, run the same command again:
+
+```bash
+bash scripts/download_dataset.sh
+```
+
+To download all five public image folds, about 26.9 GB:
+
+```bash
+CROPRO_PICAI_FOLDS="0 1 2 3 4" bash scripts/download_dataset.sh
+```
+
+To place the PI-CAI data somewhere else:
+
+```bash
+CROPRO_DATASET_ROOT="/path/to/PI-CAI" bash scripts/download_dataset.sh
+```
+
+Expected layout:
+
+```text
+dataset/PI-CAI/
+  archives/
+    picai_public_images_fold0.zip
+  images/
+    10001/
+      10001_1000001_t2w.mha
+      10001_1000001_adc.mha
+      10001_1000001_hbv.mha
+  picai_labels/
+    anatomical_delineations/whole_gland/AI/Bosma22b/
+    csPCa_lesion_delineations/human_expert/resampled/
+```
+
+Run the examples:
+
+```bash
+uv run python examples/PI-CAI_negative_crop.py
+uv run python examples/PI-CAI_positive_crop.py
+```
+
+Or run both:
+
+```bash
+bash scripts/examples.sh
+```
+
+PI-CAI notes:
+
+- Public images: `https://zenodo.org/records/6624726`
+- Labels: `https://github.com/DIAGNijmegen/picai_labels`
+- Official image names use `[patient_id]_[study_id]_t2w.mha`, `[patient_id]_[study_id]_adc.mha`, and `[patient_id]_[study_id]_hbv.mha`.
+- Whole-gland masks are used for `negative` and `unknown` crops.
+- Positive crops use the whole-gland mask plus the csPCa lesion mask. Set `tumor_label_level` to the lesion value used by the selected label file. The bundled PI-CAI positive example uses case `10032_1000032`, whose lesion label is `3`.
+
+## Command Line
+
+After installation, use the `cropro` command. From this repository, prefix commands with `uv run`.
+
+Negative or unknown patient:
+
+```bash
+uv run cropro \
+  --crop_method stride \
+  --patient_status negative \
+  --sequence_type T2W \
+  --orig_img_path_t2w data/patient_001/t2w.nii.gz \
+  --seg_img_path data/patient_001/prostate_gland_mask.nii.gz \
+  --pixel_spacing 0.4 \
+  --crop_image_size 128 \
+  --crop_stride 32 \
+  --saved_image_type png \
+  --path_to_save outputs/patient_001
+```
+
+Positive patient:
+
+```bash
+uv run cropro \
+  --crop_method stride \
+  --patient_status positive \
+  --sequence_type T2W \
+  --orig_img_path_t2w data/patient_002/t2w.nii.gz \
+  --seg_img_path data/patient_002/prostate_gland_mask.nii.gz \
+  --seg_img_path_lesion data/patient_002/lesion_mask.nii.gz \
+  --tumor_label_level 1 \
+  --c_min_positive 0.2 \
+  --pixel_spacing 0.4 \
+  --crop_image_size 128 \
+  --crop_stride 32 \
+  --saved_image_type png \
+  --path_to_save outputs/patient_002
+```
+
+Boolean CLI arguments require explicit values:
+
+```bash
+uv run cropro --keep_all_slice false --do_normalization true ...
+```
+
+## Output
+
+CROPro writes cropped files to `path_to_save`. Filenames include:
+
+- sequence type
+- slice number
+- crop index when applicable
+- crop coordinates
+- modality suffix such as `T2W`, `ADC`, or `HBV`
+
+Example:
+
+```text
+outputs/patient_001/
+  T2W_slice_7_of_21_1_cord_160_166_T2W.png
+```
+
+## Configuration Reference
+
+These variables are accepted by the Python `CropConfig` class and by CLI arguments with the same names.
+
+| Setting | Default | Meaning |
+| --- | --- | --- |
+| `crop_method` | `center` | Crop strategy: `center`, `random`, or `stride`. |
+| `orig_img_path_t2w` | `None` | T2W image path. Required for all workflows. |
+| `orig_img_path_adc` | `None` | ADC image path. Required when `sequence_type="bpMRI"`. |
+| `orig_img_path_hbv` | `None` | HBV image path. Required when `sequence_type="bpMRI"`. |
+| `seg_img_path` | `None` | Prostate gland segmentation mask path. Required for negative, unknown, and positive workflows. |
+| `seg_img_path_lesion` | `None` | Lesion segmentation mask path. Required for positive patients unless the gland mask already contains lesion labels. |
+| `prostate_gland_seg_contains_lesion` | `False` | Set to `True` when `seg_img_path` contains both gland and lesion labels. |
+| `tumor_label_level` | `2` | Label value used for lesion pixels. Use `1` if your lesion mask stores lesions as label `1`. |
+| `patient_status` | `negative` | `negative`, `positive`, or `unknown`. |
+| `pixel_spacing` | `0.5` | Target in-plane spacing in millimeters per pixel before cropping. |
+| `crop_image_size` | `128` | Output crop width and height in pixels. |
+| `sample_number` | `12` | Number of random crops to try when `crop_method="random"`. |
+| `crop_stride` | `32` | Step size in pixels when `crop_method="stride"`. |
+| `sequence_type` | `T2W` | `T2W` for T2W-only crops, or `bpMRI` for T2W/ADC/HBV crops. |
+| `normalized_image` | `True` | Set to `True` when the source image is already normalized. |
+| `normalized_vmaxNumber` | `242` | Maximum value used by the legacy normalization/saving path. |
+| `do_normalization` | `False` | Normalize image intensity before saving. |
+| `min_percentile` | `0` | Lower percentile for intensity normalization. |
+| `max_percentile` | `99.5` | Upper percentile for intensity normalization. |
+| `saved_image_type` | `tiff` | Output type: `png`, `jpg`, `jpeg`, `tiff`, `tif`, `npy`, or `nmp`. |
+| `path_to_save` | `save_crop` | Output directory. |
+| `c_min_positive` | `0.2` | Minimum lesion overlap required for saving a positive crop. |
+| `c_min_negative` | `1` | Minimum gland coverage rule used by negative crop selection. |
+| `percentage_of_allowed_overlapping_betweeing_gland_lesions_mask` | `50.0` | Allowed overlap percentage between gland and lesion masks for mask consistency checks. |
+| `number_of_slices_to_exclude_from_mask_gland` | `1` | Number of gland-mask edge slices to exclude from crop selection. |
+| `keep_all_slice` | `True` | Keep all selected slices instead of applying slice filtering. |
+
+## Project Structure
+
+```text
+CROPro/
+  src/cropro/              # Python package
+    cropping/              # Cropping implementation
+    cli.py                 # Command-line interface
+    config.py              # CropConfig dataclass
+    core.py                # CROPro runner
+  examples/                # Runnable examples
+  tests/                   # Tests
+  config/                  # Runtime configuration
+  assets/readme/           # README images
+  scripts/                 # Dataset and example scripts
+  pyproject.toml           # Package metadata and tooling config
+  uv.lock                  # Locked development environment
+```
+
+## Development
+
+Install development dependencies:
+
+```bash
+uv sync --extra dev
+```
+
+Run checks:
+
+```bash
+uv run ruff check .
+uv run pytest
+uv run python -m compileall src main.py examples tests
+uv build --no-sources
+```
+
+Before publishing, make sure the package name and version in `pyproject.toml` are correct. After publication, verify installation in a fresh project:
+
+```bash
+uv init cropro-smoke-test
+cd cropro-smoke-test
+uv add cropro
+uv run python -c "from cropro import CROPro, CropConfig; print(CropConfig().crop_method)"
+```
+
+For publishing, prefer PyPI Trusted Publishing from CI. If publishing manually, use a scoped PyPI token and avoid storing it in shell history or repository files.
+
+## Troubleshooting
+
+### `ModuleNotFoundError: No module named 'cropro'`
+
+Install the package from the repository root:
+
+```bash
+uv sync
+```
+
+Then run commands with `uv run`.
+
+### `ModuleNotFoundError: No module named 'SimpleITK'`
+
+Install dependencies:
+
+```bash
+uv sync
+```
+
+### No crops are saved
+
+Check that:
+
+- `patient_status` matches the case.
+- `seg_img_path` points to a non-empty prostate mask.
+- Positive cases include `seg_img_path_lesion`, or set `prostate_gland_seg_contains_lesion=True` if lesion labels are inside the gland mask.
+- `tumor_label_level` matches the lesion label value in the mask.
+- `crop_image_size`, `pixel_spacing`, and `c_min_positive` are not too restrictive.
+- T2W, ADC, HBV, gland mask, and lesion mask are spatially aligned.
+
+### PI-CAI download is interrupted
+
+Run the downloader again. It resumes partial archives:
+
+```bash
+bash scripts/download_dataset.sh
+```
+
+## Citation
+
+If you use CROPro, please cite:
+
+```bibtex
+@article{10.1117/1.JMI.10.2.024004,
+  author = {Alexandros Patsanis and Mohammed R. S. Sunoqrot and Tone F. Bathen and Mattijs Elschot},
+  title = {{CROPro: a tool for automated cropping of prostate magnetic resonance images}},
+  volume = {10},
+  journal = {Journal of Medical Imaging},
+  number = {2},
+  publisher = {SPIE},
+  pages = {024004},
+  year = {2023},
+  doi = {10.1117/1.JMI.10.2.024004},
+  url = {https://doi.org/10.1117/1.JMI.10.2.024004}
+}
+```
+
+## License
+
+CROPro is distributed under the MIT License. See [LICENSE](LICENSE).