brain-mapping

code for "mapping histological slice sequences to the Allen Mouse Brain Atlas without 3d reconstruction"

dataset for full brain exceeds github file size limit

to download the full package include source code and datasets use this google drive link:

For most updated information visit: web.stanford.edu/~jxiong1

Name		Name	Last commit message	Last commit date
Latest commit History 6 Commits
all_masked		all_masked
vlfeat-0.9.21		vlfeat-0.9.21
README.md		README.md
bdry_extract_3.m		bdry_extract_3.m
cea41_masked.tif		cea41_masked.tif
check_angle_result_function.m		check_angle_result_function.m
clean_data_function.m		clean_data_function.m
compute_hog_diff_lower_upper_function.m		compute_hog_diff_lower_upper_function.m
compute_hog_diff_whole_slice_function.m		compute_hog_diff_whole_slice_function.m
demo_full_brain_find_angle_and_slice_match_iterative.m		demo_full_brain_find_angle_and_slice_match_iterative.m
demo_sectional_brain_find_angle_and_slice_match_iterative.m		demo_sectional_brain_find_angle_and_slice_match_iterative.m
dist2.m		dist2.m
dp_hog_function.m		dp_hog_function.m
find_angle_iterative.m		find_angle_iterative.m
find_origin.m		find_origin.m
find_origin_nearest.m		find_origin_nearest.m
find_slice_matches_function.m		find_slice_matches_function.m
get_samples_1.m		get_samples_1.m
hist_cost_2.m		hist_cost_2.m
hungarian.m		hungarian.m
origindices.mat		origindices.mat
readme		readme
rigid_transform_2D.m		rigid_transform_2D.m
rotate_w_label.m		rotate_w_label.m
rotate_w_label_nearest.m		rotate_w_label_nearest.m
sc_compute.m		sc_compute.m
warp_with_shape.m		warp_with_shape.m

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