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Introduces TotalSegmentatorEnhanced.py and enhanced_liver_vessels.py for improved liver vessel segmentation optimized for macOS and Apple Silicon. Updates python_api.py with Mac-specific optimizations for the 'liver_vessels' task and modifies .gitignore to exclude /totalseg_env.
Introduces enhanced liver vessel post-processing with robust fallback logic, metadata output, and portal/hepatic vein splitting utilities. Adds new CLI entry point, updates setup.py, and removes legacy script. Includes new test and result data for case01 and previous runs. Updates README and .gitignore for new workflow.
Major README update: adds detailed documentation for the new enhanced liver vessel segmentation and portal/hepatic split pipeline, including installation, usage, CLI flags, outputs, limitations, and roadmap. Improves overall structure with a table of contents, clarifies installation and usage instructions, and preserves original content for other sections. This update aims to support users adopting the new pipeline and provide clearer guidance for all features.
Improves device selection and handling in TotalSegmentatorEnhanced.py, adds new CLI options for output control, and refactors main logic for enhanced liver vessel segmentation. Updates vessel_split.py with clearer seed generation, skeleton labeling, and output pruning. Moves and renames result files for consistency, and removes obsolete test and case01 files.
… and enhanced liver segmentation example
Co-authored-by: AbeezUrRehman <112747250+AbeezUrRehman@users.noreply.github.com>
…mproved Co-authored-by: AbeezUrRehman <112747250+AbeezUrRehman@users.noreply.github.com>
…3D visualization support Co-authored-by: AbeezUrRehman <112747250+AbeezUrRehman@users.noreply.github.com>
…a1-98d0-c938f5b4f100 Add TotalSegmentatorImproved CLI with organized outputs and enhanced 3D visualization support
Moved and renamed case01 files, and added new CT scan data (JSON and NIfTI) for multiple patients under structured directories. This improves dataset organization and expands the available cases for analysis.
Enhanced TotalSegmentator CLI with organized outputs, improved smoothing options, and robust mesh export functionality.
…and detailed usage for enhanced liver vessel segmentation pipeline - Introduced a structured table of contents for easier navigation. - Updated installation section with clear steps for both standard and editable installs. - Expanded usage section to include commands for enhanced liver vessel segmentation and portal/hepatic split. - Added detailed descriptions of new features, including key components and important CLI flags for the enhanced pipeline. - Retained original content for subtasks, advanced settings, and other commands while ensuring clarity and consistency.
…ormat options and enhance device argument description
- Introduced `totalseg_mpr_widget` for interactive preview and export of MPR images using sliders in Jupyter or as a standalone window. - Updated `totalseg_dicom_to_png` to support multi-plane exports (axial, coronal, sagittal) with isotropic resampling and additional options for flipping and saving. - Enhanced `TotalSegmentatorImproved` to save per-task and overall runtimes in JSON format. - Added new optional dependencies and improved error handling for DICOM file processing. - Updated documentation to reflect new features and usage instructions.
… filling, mask dilation, and minimum voxel threshold; implement placeholder STL writing for empty masks.
…enhance CLI with new export options
- Introduced `material_fix.py` script to create and apply materials based on predefined colors for various organs. - Implemented a system to normalize object names and map them to corresponding materials using regex patterns. - Enhanced `totalseg_blender_import.py` with new features including: - Centering collections to the world origin. - Improved material assignment logic with exact color palettes. - Added options for grouping imported objects into categorized collections. - Introduced remesh and transformation options during import. - Created new blend files for colored organs and scene setup.
Introduces a new Tkinter-based GUI (totalseg_gui.py) for running the medical imaging pipeline, and a Blender script (totalseg_material.py) to apply anatomical materials to scene objects. Updates TotalSegmentatorImproved.py for timezone-aware timestamps and mesh face handling, and modifies totalseg_blender_import.py to adjust default mirroring and object rotation logic.
…etup - Added package.json with dependencies for Next.js, React, Tailwind CSS, and other utilities. - Created postcss.config.mjs for Tailwind CSS integration. - Added SVG assets for UI components including file, globe, next, vercel, and window icons. - Configured TypeScript with strict settings and module resolution.
…fault path retrieval - Added functionality to select an output folder for processed results. - Implemented an API endpoint to retrieve the default Downloads folder path based on the user's OS. - Updated state management to handle output path and ensure it's validated before processing. - Improved user interface to reflect selected output path and provide feedback on folder selection. - Introduced a new Python script (run_pipeline.py) to handle the pipeline execution with real-time logging and progress updates. - Updated package-lock.json to reflect dependency changes and version upgrades.
…older handling and UI adjustments
Added web viewer scripts and assets for enhanced visualization, including setup and server scripts. Updated .gitignore to exclude node_modules, DICOM files, and data directory. Expanded README with instructions for placing medical image data. Added package.json and package-lock.json for JavaScript dependencies. Made minor updates to several Python scripts in the bin directory.
Introduces a LocaleContext for English and Japanese translations, updates TotalSegmentatorApp to use localized strings, and adds language toggle. Removes the old TotalSegmentatorApp implementation, updates layout to use Inter font and LocaleProvider, and adds translation JSON files for both languages.
Add web viewer and update documentation
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Fix process log display error and add segmentation task selector