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base repository: MouseLightPipeline/buildBrain
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base: master
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head repository: MouseLightProject/buildBrain
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compare: master
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Showing with 1,712 additions and 4,070 deletions.
  1. +8 −1 .gitignore
  2. +3 −0 .gitmodules
  3. +0 −17 NewCallback.m
  4. +0 −99 assign_frags_to_GT.m
  5. +0 −59 branch2swc.m
  6. +0 −275 buildBrain.m
  7. +0 −329 buildBrain_20181001.m
  8. +0 −275 buildBrain_workflow1.m
  9. +0 −2 buildBrain_workflow1_2018_08_01.m
  10. +0 −2 buildBrain_workflow1_2018_08_01_repeat_take_2.m
  11. +0 −2 buildBrain_workflow1_2018_08_01_sparser.m
  12. +0 −2 buildBrain_workflow1_2018_12_01.m
  13. +0 −2 buildBrain_workflow1_2018_12_01_take_2.m
  14. +0 −170 buildBrain_workflow2.m
  15. +0 −2 buildBrain_workflow2_2018_08_01.m
  16. +15 −0 build_fragments_as_mats_workflow1_2019_05_27.m
  17. +37 −0 build_fragments_as_single_mat_2019_05_27.m
  18. +24 −0 build_full_trees_as_named_tree_mats_2018_10_01.m
  19. +19 −0 build_full_trees_as_named_tree_mats_2018_10_01_will_p_map.m
  20. +20 −0 build_full_trees_as_named_tree_mats_2018_10_01_will_p_map_set_2.m
  21. +36 −0 build_full_trees_as_named_tree_mats_2019_05_27.m
  22. +20 −0 build_full_trees_as_named_tree_mats_2019_08_08.m
  23. +39 −0 build_full_trees_as_named_tree_mats_2019_09_06.m
  24. +43 −0 build_full_trees_as_named_tree_mats_2019_10_04.m
  25. +46 −0 build_full_trees_as_named_tree_mats_2019_10_04_debug.m
  26. +43 −0 build_full_trees_as_named_tree_mats_2019_10_04_take_2.m
  27. +203 −0 build_full_trees_as_named_tree_mats_2019_12_25.m
  28. +19 −0 build_full_trees_as_named_tree_mats_2020_01_13.m
  29. +203 −0 build_full_trees_as_named_tree_mats_2020_01_23.m
  30. +199 −0 build_full_trees_as_named_tree_mats_2020_01_28.m
  31. +199 −0 build_full_trees_as_named_tree_mats_2020_01_28_cameron_p_map.m
  32. +19 −0 build_full_trees_as_named_tree_mats_2020_02_24.m
  33. +0 −5 checkQuant.m
  34. +37 −0 check_full_tree_lattice_alignment_2020_01_28_cameron_p_map.m
  35. +24 −34 common/+graphfuncs/buildgraph.m
  36. BIN common/graphalgs.mexa64
  37. +9 −9 common/imageproc/pix2um.m
  38. +26 −0 common/imageproc/um_from_voxels.m
  39. +11 −35 common/morpho/{getBranches.m → getBranchesOld.m}
  40. +48 −41 common/morpho/prunTree.m
  41. +49 −0 common/morpho/prune_tree_old.m
  42. +0 −120 common/morpho/sampleTree.m
  43. +3 −3 common/morpho/{smoothtree.m → smoothtreeold.m}
  44. +53 −53 common/visual/gplot3.m
  45. +0 −29 config_files/config_buildBrain_161031.cfg
  46. +0 −33 config_files/config_buildBrain_20150619_octant12_prob0.cfg
  47. +0 −34 config_files/config_buildBrain_20170419_prob0.cfg
  48. +0 −34 config_files/config_buildBrain_20170504_prob0.cfg
  49. +0 −34 config_files/config_buildBrain_20170628_prob0.cfg
  50. +0 −34 config_files/config_buildBrain_20170810_prob1.cfg
  51. +0 −34 config_files/config_buildBrain_20170911_prob0.cfg
  52. +0 −34 config_files/config_buildBrain_20170925_prob0.cfg
  53. +0 −34 config_files/config_buildBrain_20170925_prob0_stratum.cfg
  54. +0 −34 config_files/config_buildBrain_20171031_prob0.cfg
  55. +0 −34 config_files/config_buildBrain_20180309_prob0.cfg
  56. +0 −34 config_files/config_buildBrain_20180309_prob1.cfg
  57. +0 −34 config_files/config_buildBrain_20180413_prob0.cfg
  58. +0 −34 config_files/config_buildBrain_20180413_prob0_200.cfg
  59. +0 −34 config_files/config_buildBrain_20180523_prob0_200.cfg
  60. +0 −34 config_files/config_buildBrain_20180702_prob0_100.cfg
  61. +0 −34 config_files/config_buildBrain_20180801_prob0.cfg
  62. +0 −42 config_files/config_buildBrain_20180801_prob0_repeat.cfg
  63. +0 −42 config_files/config_buildBrain_20180801_prob0_repeat_affinity.cfg
  64. +0 −45 config_files/config_buildBrain_20180801_prob0_repeat_sparser.cfg
  65. +0 −42 config_files/config_buildBrain_20180801_prob0_repeat_take_2.cfg
  66. +0 −34 config_files/config_buildBrain_20180815_prob0.cfg
  67. +0 −34 config_files/config_buildBrain_20181001_prob0.cfg
  68. +0 −34 config_files/config_buildBrain_20181201_prob0.cfg
  69. +0 −34 config_files/config_buildBrain_20181201_prob0_take_2.cfg
  70. +6 −0 convert_full_trees_to_swc_2020_01_28.m
  71. +6 −0 convert_full_trees_to_swc_2020_01_28_cameron_p_map.m
  72. +80 −0 extract_frags_near_consensus_neurons_2018_10_01_will_settings_2.m
  73. +0 −14 filterEdges.m
  74. +0 −420 functions/affinityBuilder.m
  75. +0 −29 functions/filterGraph.m
  76. +0 −15 functions/getIndsinROI.m
  77. +0 −72 functions/loadGT.m
  78. +0 −122 functions/maskWithAllenAtlas.m
  79. +0 −32 functions/neuron_branch_assignment.m
  80. +0 −57 functions/pruneGraph.m
  81. +0 −50 functions/skel2graph.m
  82. +0 −282 functions/workflow1.m
  83. +0 −316 functions/workflow2.m
  84. +18 −0 gen_frags_with_5_or_more_nodes_for_2020_01_28_cam_p_map_as_swcs.m
  85. +19 −0 gen_frags_with_5p_nodes_for_2018_10_01_will_p_map_as_mats_2.m
  86. +18 −0 gen_frags_with_5p_nodes_for_2018_10_01_will_p_map_as_swcs.m
  87. +18 −0 gen_frags_with_5p_nodes_for_2018_10_01_will_p_map_as_swcs_2.m
  88. +18 −0 generate_fragments_with_5_or_more_nodes_for_2019_08_08_as_swcs.m
  89. +18 −0 generate_fragments_with_5_or_more_nodes_for_2020_01_13_as_swcs.m
  90. +18 −0 generate_fragments_with_5_or_more_nodes_for_2020_01_23_as_swcs.m
  91. +18 −0 generate_fragments_with_5_or_more_nodes_for_2020_01_28_as_swcs.m
  92. +18 −0 generate_fragments_with_5_or_more_nodes_for_2020_02_24_as_swcs.m
  93. +0 −36 junk_ids_052318.m
  94. +0 −72 junk_ids_070218sample.m
  95. +0 −10 loadSwcFolder.m
  96. +0 −22 maskEdges.m
  97. +0 −10 maskWithInputLocations.m
  98. +1 −0 modpath.m
  99. +1 −0 mouselight_toolbox
  100. +0 −67 scripts/cropSectionBasedOnGT.m
  101. +0 −7 test.swc
  102. +0 −21 vizClustersforJunks.m
9 changes: 8 additions & 1 deletion .gitignore
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@@ -1,4 +1,11 @@
*.mat
*.tif
/temp/
temp
*.m~
parfor_progress.txt
*.stdout
*.stderr
*.stdouterr
2019-04-17-reduced-skeleton
*.out.txt

3 changes: 3 additions & 0 deletions .gitmodules
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[submodule "mouselight_toolbox"]
path = mouselight_toolbox
url = https://github.com/MouseLightProject/mouselight_toolbox
17 changes: 0 additions & 17 deletions NewCallback.m
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99 changes: 0 additions & 99 deletions assign_frags_to_GT.m
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59 changes: 0 additions & 59 deletions branch2swc.m
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