User Guides

We are in the process of consolidating the code and moving them to a new repository.

For technical details, please reference the following paper:

The Active Atlas: Combining 3D Anatomical Models with Texture Detectors, Yuncong Chen et al., MICCAI 2017 [pdf]

Explanations for how to install and run the code, intended for the non-programmer, are in the User Guide.

Code Structure

annotation: code related to processing human annotations
gui: code for two GUIs
- brain labeling GUI (used to annotate landmarks in brain)
- preprocessing GUI: processing raw images, remoing background, aligning stack.
learning: code for extracting patches, generating features, training classifiers and processing score maps
preprocess: code for preprocessing
reconstruct: code for reconstructing volumes
registration: code for 3D registration
utilities: utilities code
visualization: notebook for testing visualization code
web_service: code for the web service that accept request for preprocessing and other tasks from GUI.
intensity: codes for running intensity-based registration methods (via third-party program elastix).

spm: experiments about represent textures using SPM (Spatial Pyramid Matching)
snake: experiments about active contour methods
adaboost_m2
cells: classification using cell-based texture descriptors.
dictionary: experiments for dictionary learning methods.
new_region:

Name		Name	Last commit message	Last commit date
Latest commit History 2,299 Commits
3d		3d
annotation		annotation
aws		aws
demo		demo
deprecated		deprecated
doc		doc
gui		gui
intensity		intensity
learning		learning
preprocess		preprocess
reconstruct		reconstruct
registration		registration
side_projects		side_projects
utilities		utilities
visualization		visualization
writeup		writeup
.gitignore		.gitignore
README.md		README.md
annotation_pipeline.ipynb		annotation_pipeline.ipynb
automatic_annotation_evaluation.csv		automatic_annotation_evaluation.csv
create_sql_database.ipynb		create_sql_database.ipynb
functions_for_stacy.ipynb		functions_for_stacy.ipynb
mhd_utils_3d.py		mhd_utils_3d.py
move_s3_files.ipynb		move_s3_files.ipynb
pipeline_aws.ipynb		pipeline_aws.ipynb
preprocess_pipeline_aws.ipynb		preprocess_pipeline_aws.ipynb
preprocess_pipeline_aws_thalamus.ipynb		preprocess_pipeline_aws_thalamus.ipynb
requirements.txt		requirements.txt