GitHub - MouseLightProject/mouselight_toolbox: A Matlab toolbox for doing MouseLight-y things

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Name	Name	Last commit message	Last commit date
Latest commit adamltaylor master: Added example sample-processing folder sample-2022-02-01, to … Apr 4, 2024 5288524 · Apr 4, 2024 History 128 Commits
.dvc	.dvc	Added DVC remote on dm11	Apr 8, 2022
check-tiles	check-tiles	Added zero-tile checks in a couple places	Mar 31, 2022
common	common	Refactored vizMatchALT.m into visualize_xy_matching_after_loading_sta…	Jan 13, 2022
foreground-classifiers	foreground-classifiers	Added .dvc files for foreground classifier data files	Apr 8, 2022
freezing	freezing	Updated shell script to use Matlab 2023a, which exits and works on up…	Oct 10, 2023
landmark-matching	landmark-matching	Fixed bug in landmark-matching/pointmatch.m, added debugging output t…	Apr 20, 2022
line-fix	line-fix	Changes related to bqueue_type adding option to run locally and outsi…	Apr 11, 2023
rendering	rendering	Functions for visualize z-matching, folded in Matlab wrapper for rend…	Jan 24, 2022
sample-2022-02-01	sample-2022-02-01	master: Added example sample-processing folder sample-2022-02-01, to …	Apr 4, 2024
stitching	stitching	Fixed bug in stitching/compute_targets_from_z_matches.m	Mar 4, 2022
tmt @ c303b07	tmt @ c303b07	Updated to latest tmt	Sep 27, 2023
.dvcignore	.dvcignore	Initialized DVC	Apr 8, 2022
.gitignore	.gitignore	Folded in http://github.com/MouseLightProject/freezing repo as of com…	Sep 27, 2023
.gitmodules	.gitmodules	Added tmt as submodule, updated modpath.m appropriately	Feb 11, 2022
adjacency_from_forest_as_named_trees.m	adjacency_from_forest_as_named_trees.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
affine_from_cpg_targets.m	affine_from_cpg_targets.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
are_md5s_the_same.m	are_md5s_the_same.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
are_paired_descriptors_close_enough.m	are_paired_descriptors_close_enough.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
bag_items_by_id.m	bag_items_by_id.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
barycentric_interpolant.m	barycentric_interpolant.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
base_name_from_file_name.m	base_name_from_file_name.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
bits_from_chunk_ijk0.m	bits_from_chunk_ijk0.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
bits_from_octree_path.m	bits_from_octree_path.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
build_full_trees_as_named_tree_mats.m	build_full_trees_as_named_tree_mats.m	Updated code to use new version of progress_bar_object.m	Jan 12, 2022
build_full_trees_as_named_tree_mats_function.m	build_full_trees_as_named_tree_mats_function.m	Updated code to use new version of progress_bar_object.m	Jan 12, 2022
build_raw_tile_index.m	build_raw_tile_index.m	Added zero-tile checks in a couple places	Mar 31, 2022
build_raw_tile_index_for_neighborhood.m	build_raw_tile_index_for_neighborhood.m	Added all the stuff for stitching	Dec 14, 2021
build_tile_index_dirwalk_callback.m	build_tile_index_dirwalk_callback.m	Added code for doing line-shifting in-place	Mar 3, 2022
chain_length_from_chain.m	chain_length_from_chain.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
chains_from_rooted_tree.m	chains_from_rooted_tree.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
chains_from_rooted_tree_in_place.m	chains_from_rooted_tree_in_place.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
chains_from_rooted_tree_with_id_tracking.m	chains_from_rooted_tree_with_id_tracking.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
chains_from_tree.m	chains_from_tree.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
chains_from_tree_in_place.m	chains_from_tree_in_place.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
chains_from_tree_with_id_tracking.m	chains_from_tree_with_id_tracking.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
channel_index0_as_string_from_tile_file_name.m	channel_index0_as_string_from_tile_file_name.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
chunk_bounding_box_from_bounding_box.m	chunk_bounding_box_from_bounding_box.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
chunk_ijk0_from_bits.m	chunk_ijk0_from_bits.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
chunk_ijk1s_from_octree_paths.m	chunk_ijk1s_from_octree_paths.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
clean_up_skeleton_component.m	clean_up_skeleton_component.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
clean_up_skeleton_graph.m	clean_up_skeleton_graph.m	Updated code to use new version of progress_bar_object.m	Jan 12, 2022
collect_fragments_into_single_mat_file.m	collect_fragments_into_single_mat_file.m	Updated code to use new version of progress_bar_object.m	Jan 12, 2022
collect_landmarks.m	collect_landmarks.m	Added a few functions	Dec 8, 2021
collect_z_face_matches.m	collect_z_face_matches.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
compute_affine_landmark_match_distance.m	compute_affine_landmark_match_distance.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
compute_affine_landmark_match_error.m	compute_affine_landmark_match_error.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
compute_barycentric_landmark_match_distance.m	compute_barycentric_landmark_match_distance.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
compute_barycentric_landmark_match_error.m	compute_barycentric_landmark_match_error.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
compute_landmarks.sh	compute_landmarks.sh	Updated shell script to use Matlab 2023a, which exits and works on up…	Oct 10, 2023
compute_landmarks_for_all_tile_channels.m	compute_landmarks_for_all_tile_channels.m	Added compute_landmarks_for_all_tile_channels.m for Patrick pipeline use	Apr 8, 2022
compute_landmarks_for_patrick_pipeline.m	compute_landmarks_for_patrick_pipeline.m	Fixed argument-order bug in compute_landmarks_for_patrick_pipeline.m	Apr 12, 2022
compute_or_read_from_memo.m	compute_or_read_from_memo.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
compute_z_matches.sh	compute_z_matches.sh	Updated shell script to use Matlab 2023a, which exits and works on up…	Oct 10, 2023
compute_z_matches_for_patrick_pipeline.m	compute_z_matches_for_patrick_pipeline.m	Fixed bug in landmark-matching/pointmatch.m, added debugging output t…	Apr 20, 2022
connected_components_with_fractionation.m	connected_components_with_fractionation.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
connected_components_without_fractionation.m	connected_components_without_fractionation.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
convert_full_named_trees_as_mat_to_swc.m	convert_full_named_trees_as_mat_to_swc.m	Updated code to use new version of progress_bar_object.m	Jan 12, 2022
convert_named_tree_to_jaws_coords.m	convert_named_tree_to_jaws_coords.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
convert_named_trees_to_jaws_coords.m	convert_named_trees_to_jaws_coords.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
convert_swc_array_to_jaws_coords.m	convert_swc_array_to_jaws_coords.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
convert_swc_arrays_to_jaws_coords.m	convert_swc_arrays_to_jaws_coords.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
copy_raw_tile_neighborhood.m	copy_raw_tile_neighborhood.m	Added code for doing line-shifting in-place	Mar 3, 2022
copy_raw_tile_neighborhood_as_links.m	copy_raw_tile_neighborhood_as_links.m	Added code for doing line-shifting in-place	Mar 3, 2022
correctTiles.m	correctTiles.m	Functions for visualize z-matching, folded in Matlab wrapper for rend…	Jan 24, 2022
decimate_chain.m	decimate_chain.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
decimate_chains.m	decimate_chains.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
defragment_node_ids_in_edges.m	defragment_node_ids_in_edges.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
directed_adjacency_from_edges.m	directed_adjacency_from_edges.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
directed_adjacency_from_forest_of_named_trees.m	directed_adjacency_from_forest_of_named_trees.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
directed_adjacency_from_named_tree.m	directed_adjacency_from_named_tree.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
does_file_name_end_in_dot_mj2.m	does_file_name_end_in_dot_mj2.m	Consolidating find_and_*.m functions	May 22, 2023
does_file_name_end_in_dot_tif.m	does_file_name_end_in_dot_tif.m	Consolidating find_and_*.m functions	May 22, 2023
does_file_name_end_in_dot_tif_and_mj2_is_missing.m	does_file_name_end_in_dot_tif_and_mj2_is_missing.m	Fixed very dumb bug in does_file_name_end_in_dot_tif_and_mj2_is_missi…	May 17, 2023
does_file_name_match_certificate_file.m	does_file_name_match_certificate_file.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
does_file_name_not_end_in_dot_mj2.m	does_file_name_not_end_in_dot_mj2.m	Consolidating find_and_*.m functions	May 22, 2023
does_file_name_not_end_in_dot_tif.m	does_file_name_not_end_in_dot_tif.m	Consolidating find_and_*.m functions	May 22, 2023
does_match_channel_0_raw_tile_tif_name.m	does_match_channel_0_raw_tile_tif_name.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
does_match_raw_tile_tif_name.m	does_match_raw_tile_tif_name.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
does_match_regexp.m	does_match_regexp.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
does_md5_match.m	does_md5_match.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
does_not_match_raw_tile_tif_name.m	does_not_match_raw_tile_tif_name.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
dogDescriptor.m	dogDescriptor.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
edges_from_chains.m	edges_from_chains.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
edges_from_named_tree.m	edges_from_named_tree.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
empty_named_tree_struct.m	empty_named_tree_struct.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
extract_tiles_near_tile.m	extract_tiles_near_tile.m	Updated code to use new version of progress_bar_object.m	Jan 12, 2022
figure_mip.m	figure_mip.m	Added a few functions	Dec 8, 2021
figure_to_check_alignment_to_stack.m	figure_to_check_alignment_to_stack.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
file_accumulate_map_filter.m	file_accumulate_map_filter.m	Consolidating find_and_*.m functions	May 22, 2023
file_path_from_chunk_path.m	file_path_from_chunk_path.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
file_path_from_tile_path.m	file_path_from_tile_path.m	Functions for visualize z-matching, folded in Matlab wrapper for rend…	Jan 24, 2022
file_relative_path_from_tile_relative_path.m	file_relative_path_from_tile_relative_path.m	Functions for visualize z-matching, folded in Matlab wrapper for rend…	Jan 24, 2022
find_and_batch.m	find_and_batch.m	Consolidating find_and_*.m functions	May 22, 2023
find_and_list.m	find_and_list.m	Consolidating find_and_*.m functions	May 22, 2023
find_and_verify.m	find_and_verify.m	Added identifier to one error, got latest tmt	May 22, 2023
find_fragments_near_neuron.m	find_fragments_near_neuron.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
find_fragments_near_neurons.m	find_fragments_near_neurons.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
find_label_and_get_value_in_acquisition_file.m	find_label_and_get_value_in_acquisition_file.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
fraction_of_xyzs_at_voxel_centers_using_erhan_conventions.m	fraction_of_xyzs_at_voxel_centers_using_erhan_conventions.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
generate_fragments.m	generate_fragments.m	Updated code to use new version of progress_bar_object.m	Jan 12, 2022
generate_fragments_as_named_trees_from_named_tree.m	generate_fragments_as_named_trees_from_named_tree.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
generate_fragments_as_one_mat_per_tree.m	generate_fragments_as_one_mat_per_tree.m	Updated code to use new version of progress_bar_object.m	Jan 12, 2022
generate_fragments_as_swcs.m	generate_fragments_as_swcs.m	Got rid of parfor_progress(), which didn't work well for multiple sim…	Jan 7, 2022
generate_fragments_as_swcs_from_named_tree_old.m	generate_fragments_as_swcs_from_named_tree_old.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
generate_fragments_from_named_tree.m	generate_fragments_from_named_tree.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
generate_fragments_higher_level.m	generate_fragments_higher_level.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
get_file_size.m	get_file_size.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
get_mouselight_rendered_substack.m	get_mouselight_rendered_substack.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
get_mouselight_rendered_substack_simple.m	get_mouselight_rendered_substack_simple.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
get_tiff_shape.m	get_tiff_shape.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
get_tile_flip_state.m	get_tile_flip_state.m	Added code for doing line-shifting in-place	Mar 3, 2022
hashy.m	hashy.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
imagery_file_relative_path_from_relative_path.m	imagery_file_relative_path_from_relative_path.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
index_using_rows.m	index_using_rows.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
interpolate_chain.m	interpolate_chain.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
interpolate_chain_xyzs.m	interpolate_chain_xyzs.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
interpolate_chains.m	interpolate_chains.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
interpolate_forest_of_named_trees.m	interpolate_forest_of_named_trees.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
interpolate_named_tree.m	interpolate_named_tree.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
interpolate_named_tree_old.m	interpolate_named_tree_old.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
interpolate_tree.m	interpolate_tree.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
invert_map_array.m	invert_map_array.m	Added run_some_tiles_through_1234_stages.m	Dec 13, 2021
invert_parent_from_node_id.m	invert_parent_from_node_id.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
invert_parent_from_node_index.m	invert_parent_from_node_index.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
invert_partial_map_array.m	invert_partial_map_array.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
is_checkpoint_file_present.m	is_checkpoint_file_present.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
landmark_file_name_from_tile_relative_path.m	landmark_file_name_from_tile_relative_path.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
load_forest_from_folder_of_mats.m	load_forest_from_folder_of_mats.m	Got rid of parfor_progress(), which didn't work well for multiple sim…	Jan 7, 2022
load_forest_from_folder_of_named_tree_mats.m	load_forest_from_folder_of_named_tree_mats.m	Got rid of parfor_progress(), which didn't work well for multiple sim…	Jan 7, 2022
load_landmark_file.m	load_landmark_file.m	Fixed bug with empty input to load_landmark_file()	Jun 27, 2022
load_mouselight_rendered_chunk.m	load_mouselight_rendered_chunk.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
load_named_tree_from_mat.m	load_named_tree_from_mat.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
load_sample_shape_origin_and_spacing.m	load_sample_shape_origin_and_spacing.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
load_sample_shape_origin_and_spacing_old.m	load_sample_shape_origin_and_spacing_old.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
load_swc.m	load_swc.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
load_swc_as_named_tree.m	load_swc_as_named_tree.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
lpl_process_single_tile.m	lpl_process_single_tile.m	Added all the stuff for stitching	Dec 14, 2021
lpl_process_single_tile_channel.m	lpl_process_single_tile_channel.m	Added all the stuff for stitching	Dec 14, 2021
make_raw_tile_folder_for_tile_neighborhood.m	make_raw_tile_folder_for_tile_neighborhood.m	Added all the stuff for stitching	Dec 14, 2021
make_raw_tile_index_for_tile_neighborhood.m	make_raw_tile_index_for_tile_neighborhood.m	Added all the stuff for stitching	Dec 14, 2021
md5sum.m	md5sum.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
modpath.m	modpath.m	Updated modpath.m to pick up freezing/	Sep 27, 2023
montage_from_stack_ijk.m	montage_from_stack_ijk.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
move_to_backup.m	move_to_backup.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
named_forest_of_fragments_from_named_tree.m	named_forest_of_fragments_from_named_tree.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
named_tree_from_tree_as_dA_struct.m	named_tree_from_tree_as_dA_struct.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
named_tree_from_undirected_graph.m	named_tree_from_undirected_graph.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
natsort.m	natsort.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
neighbors_from_node_index_from_adjacency.m	neighbors_from_node_index_from_adjacency.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
new_named_tree.m	new_named_tree.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
nop.m	nop.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
octree_path_from_bits.m	octree_path_from_bits.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
octree_path_from_ijk1.m	octree_path_from_ijk1.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
octree_paths_from_chunk_ijk1s.m	octree_paths_from_chunk_ijk1s.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
p_map_file_relative_path_from_relative_path.m	p_map_file_relative_path_from_relative_path.m	Added a few functions	Dec 8, 2021
path_object.m	path_object.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
plot_graph.m	plot_graph.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
plot_mip.m	plot_mip.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
point_cloud_from_forest.m	point_cloud_from_forest.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
point_cloud_from_forest_as_named_trees.m	point_cloud_from_forest_as_named_trees.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
preallocate_forest_of_named_trees.m	preallocate_forest_of_named_trees.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
prune_tree.m	prune_tree.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
prune_tree_in_place.m	prune_tree_in_place.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
prune_tree_with_id_tracking.m	prune_tree_with_id_tracking.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
random_line_shift.m	random_line_shift.m	Added code for doing line-shifting in-place	Mar 3, 2022
read_16bit_grayscale_mj2.m	read_16bit_grayscale_mj2.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
read_16bit_grayscale_tif.m	read_16bit_grayscale_tif.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
read_channel_semantics_file.m	read_channel_semantics_file.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
read_fov_shape_from_acquisition_file.m	read_fov_shape_from_acquisition_file.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
read_lattice_position_from_acquisition_file.m	read_lattice_position_from_acquisition_file.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
read_metadata_file.m	read_metadata_file.m	Added code for doing line-shifting in-place	Mar 3, 2022
read_old_style_sample_metadata.m	read_old_style_sample_metadata.m	Added code for doing line-shifting in-place	Mar 3, 2022
read_original_sample_metadata.m	read_original_sample_metadata.m	Added code for doing line-shifting in-place	Mar 3, 2022
read_post_line_fix_sample_metadata.m	read_post_line_fix_sample_metadata.m	Added code for doing line-shifting in-place	Mar 3, 2022
read_renderer_calculated_parameters_file.m	read_renderer_calculated_parameters_file.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
read_sample_metadata_robustly.m	read_sample_metadata_robustly.m	Added code for doing line-shifting in-place	Mar 3, 2022
read_tile_metadata.m	read_tile_metadata.m	Added code for doing line-shifting in-place	Mar 3, 2022
relpath.m	relpath.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
replace_extension.m	replace_extension.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
rooted_tree_from_connected_graph.m	rooted_tree_from_connected_graph.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
run_all_tiles_through_1234_stages.m	run_all_tiles_through_1234_stages.m	Changes related to bqueue_type adding option to run locally and outsi…	Apr 11, 2023
run_some_tiles_through_1234_stages.m	run_some_tiles_through_1234_stages.m	Changes related to bqueue_type adding option to run locally and outsi…	Apr 11, 2023
sample_rendered_data.m	sample_rendered_data.m	Updated code to use new version of progress_bar_object.m	Jan 12, 2022
save_named_tree.m	save_named_tree.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
save_named_tree_as_mat.m	save_named_tree_as_mat.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
save_named_tree_as_swc.m	save_named_tree_as_swc.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
save_skeleton_graph_as_text.m	save_skeleton_graph_as_text.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
save_somata_as_multiple_swcs.m	save_somata_as_multiple_swcs.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
save_somata_as_multiple_swcs_with_auto_names.m	save_somata_as_multiple_swcs_with_auto_names.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
save_somata_as_single_swc.m	save_somata_as_single_swc.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
save_swc.m	save_swc.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
save_swc_arrays.m	save_swc_arrays.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
save_swc_from_named_tree.m	save_swc_from_named_tree.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
save_swcs_from_named_trees.m	save_swcs_from_named_trees.m	Got rid of parfor_progress(), which didn't work well for multiple sim…	Jan 7, 2022
simple_dir.m	simple_dir.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
skel2graph.m	skel2graph.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
skel2graph_core.m	skel2graph_core.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
smooth_chain.m	smooth_chain.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
smooth_chains.m	smooth_chains.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
sort_components_by_size.m	sort_components_by_size.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
struct_with_shape_and_fields.m	struct_with_shape_and_fields.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
swc_array_from_named_tree.m	swc_array_from_named_tree.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
tile_relative_path_from_tile_file_path.m	tile_relative_path_from_tile_file_path.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
tile_relative_path_from_tile_folder_path.m	tile_relative_path_from_tile_folder_path.m	Functions for visualize z-matching, folded in Matlab wrapper for rend…	Jan 24, 2022
tree_as_swc_array_from_tree_as_struct.m	tree_as_swc_array_from_tree_as_struct.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
tree_from_component_as_function.m	tree_from_component_as_function.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
undirected_adjacency_from_edges.m	undirected_adjacency_from_edges.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
use_this_fraction_of_cores.m	use_this_fraction_of_cores.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
use_this_many_cores.m	use_this_many_cores.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
writeYML.m	writeYML.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
write_16bit_grayscale_mj2.m	write_16bit_grayscale_mj2.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
write_16bit_grayscale_tif.m	write_16bit_grayscale_tif.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
write_8bit_grayscale_tif.m	write_8bit_grayscale_tif.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
write_file_from_cellstring.m	write_file_from_cellstring.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
write_metadata_file.m	write_metadata_file.m	Added code for doing line-shifting in-place	Mar 3, 2022
write_nbit_grayscale_tif.m	write_nbit_grayscale_tif.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
write_post_line_fix_sample_metadata.m	write_post_line_fix_sample_metadata.m	Added code for doing line-shifting in-place	Mar 3, 2022
write_string_to_file.m	write_string_to_file.m	Moved code from https://github.com/JaneliaSciComp/tmt/mouselighty to …	Dec 8, 2021
write_tile_metadata.m	write_tile_metadata.m	Added code for doing line-shifting in-place	Mar 3, 2022