Name		Name	Last commit message	Last commit date
Latest commit History 52 Commits
BOOTSTRAP_PLOTS_FOR_FIGURE.ipynb		BOOTSTRAP_PLOTS_FOR_FIGURE.ipynb
Lens_python_conformal_mapping_demo.ipynb		Lens_python_conformal_mapping_demo.ipynb
MAKE_ALIGNMENT_PHOTOS.ipynb		MAKE_ALIGNMENT_PHOTOS.ipynb
MAKE_ALT_GENOTYPE_STATISTICS_FIGURES.ipynb		MAKE_ALT_GENOTYPE_STATISTICS_FIGURES.ipynb
MAKE_ALT_GENOTYPE_STATISTICS_FIGURES_LINEARSHEARALIGN.ipynb		MAKE_ALT_GENOTYPE_STATISTICS_FIGURES_LINEARSHEARALIGN.ipynb
MAKE_ALT_GENOTYPE_STATISTICS_FIGURES_TREEFINAL.ipynb		MAKE_ALT_GENOTYPE_STATISTICS_FIGURES_TREEFINAL.ipynb
MAKE_CELL_SIZE_AND_NUMBER_FIGURES.ipynb		MAKE_CELL_SIZE_AND_NUMBER_FIGURES.ipynb
MAKE_FIGURE_FOR_PREPROCESSING.ipynb		MAKE_FIGURE_FOR_PREPROCESSING.ipynb
MAKE_FLY_NORMAL_VECTOR_AND_HEIGHT_PLOTS.ipynb		MAKE_FLY_NORMAL_VECTOR_AND_HEIGHT_PLOTS.ipynb
MAKE_GENOTYPE_SPREAD_EROSION_PLOTS.ipynb		MAKE_GENOTYPE_SPREAD_EROSION_PLOTS.ipynb
MAKE_INTERGENOTYPE_TPEDIFF_FIGURES.ipynb		MAKE_INTERGENOTYPE_TPEDIFF_FIGURES.ipynb
MAKE_PREPROCESS_SUPPLEMENTAL_ALIGNMENT_FIG.ipynb		MAKE_PREPROCESS_SUPPLEMENTAL_ALIGNMENT_FIG.ipynb
MAKE_SMOOTHING_PREPROCESS_FIGURES.ipynb		MAKE_SMOOTHING_PREPROCESS_FIGURES.ipynb
README.md		README.md
README_ALIGNMENTPIPELINE_NONCLUSTERBIT.docx		README_ALIGNMENTPIPELINE_NONCLUSTERBIT.docx
README_ALIGNMENTPIPELINE_NONCLUSTERBIT.txt		README_ALIGNMENTPIPELINE_NONCLUSTERBIT.txt
README_DEPRACATEDFILES_NONCOMPREHENSIVE.docx		README_DEPRACATEDFILES_NONCOMPREHENSIVE.docx
README_DEPRACATEDFILES_NONCOMPREHENSIVE.txt		README_DEPRACATEDFILES_NONCOMPREHENSIVE.txt
README_FlyCellStatisticsAndHistograms.docx		README_FlyCellStatisticsAndHistograms.docx
README_FlyCellStatisticsAndHistograms.txt		README_FlyCellStatisticsAndHistograms.txt
README_FlyWingCurvature.docx		README_FlyWingCurvature.docx
README_FourierTransformsandCorrelations.docx		README_FourierTransformsandCorrelations.docx
README_FourierTransformsandCorrelations.txt		README_FourierTransformsandCorrelations.txt
README_MEANBACKALIGN.docx		README_MEANBACKALIGN.docx
README_MEANBACKALIGN.txt		README_MEANBACKALIGN.txt
README_ManualCorrection.docx		README_ManualCorrection.docx
README_ManualCorrection.txt		README_ManualCorrection.txt
README_PythonEnvironment.docx		README_PythonEnvironment.docx
README_PythonEnvironment.txt		README_PythonEnvironment.txt
REAME_FlyWingCurvature.txt		REAME_FlyWingCurvature.txt
VertexModelOutputToShapely-dev.ipynb		VertexModelOutputToShapely-dev.ipynb
VertexModel_SHEARMODULUS_DEBUG.ipynb		VertexModel_SHEARMODULUS_DEBUG.ipynb
WT_01_Study_littlea_calculation_and_sharpness_in_standard_deviation-02-20-23.ipynb		WT_01_Study_littlea_calculation_and_sharpness_in_standard_deviation-02-20-23.ipynb
WT_02_wings_vein_variability_study.ipynb		WT_02_wings_vein_variability_study.ipynb
WT_wings_vein_variability_study.ipynb		WT_wings_vein_variability_study.ipynb
align-wings-123.ipynb		align-wings-123.ipynb
align-wings-125.ipynb		align-wings-125.ipynb
align-wings-136.ipynb		align-wings-136.ipynb
align-wings-146.ipynb		align-wings-146.ipynb
align-wings-WT-02.ipynb		align-wings-WT-02.ipynb
align-wings.ipynb		align-wings.ipynb
bootstrapping_testing.ipynb		bootstrapping_testing.ipynb
boundary_smoothing_study.ipynb		boundary_smoothing_study.ipynb
bristle-data-mondal-2025.yml		bristle-data-mondal-2025.yml
cell-fourier-transform-experiment-REALWINGS-SHAPELY-JAN2025-UPDATE.ipynb		cell-fourier-transform-experiment-REALWINGS-SHAPELY-JAN2025-UPDATE.ipynb
cell-fourier-transform-experiment-REALWINGS-SHAPELY.ipynb		cell-fourier-transform-experiment-REALWINGS-SHAPELY.ipynb
cell-fourier-transform-experiment-REALWINGS.ipynb		cell-fourier-transform-experiment-REALWINGS.ipynb
cell-fourier-transform-experiment.ipynb		cell-fourier-transform-experiment.ipynb
cell-pattern-analysis-PROBECORRELATIONS.ipynb		cell-pattern-analysis-PROBECORRELATIONS.ipynb
cell-pattern-analysis-REALWINGS-SHAPELY-DEV.ipynb		cell-pattern-analysis-REALWINGS-SHAPELY-DEV.ipynb
cell_pattern_analysis-REALWINGS-ALLGENOTYPE-PAPERFIGURES.ipynb		cell_pattern_analysis-REALWINGS-ALLGENOTYPE-PAPERFIGURES.ipynb
cell_pattern_analysis-REALWINGS-ALLGENOTYPE.ipynb		cell_pattern_analysis-REALWINGS-ALLGENOTYPE.ipynb
cell_size_statistics_and_histograms.ipynb		cell_size_statistics_and_histograms.ipynb
compartment-wise-CD-SEPARATEDCOMPARTMENTS-batch-stats-analysis.ipynb		compartment-wise-CD-SEPARATEDCOMPARTMENTS-batch-stats-analysis.ipynb
compartment-wise-Frankensteins-Wing-dev.ipynb		compartment-wise-Frankensteins-Wing-dev.ipynb
compartment-wise-LSA-TREEALIGNMENT-DEV.ipynb		compartment-wise-LSA-TREEALIGNMENT-DEV.ipynb
compartment-wise-LSA-WT-SH-batch-stats-analysis.ipynb		compartment-wise-LSA-WT-SH-batch-stats-analysis.ipynb
compartment-wise-LSA-allwing-HEAVILYSHEAREDCOMPARTMENTS-analysis.ipynb		compartment-wise-LSA-allwing-HEAVILYSHEAREDCOMPARTMENTS-analysis.ipynb
compartment-wise-LSA-calculate-intergenotype-distances.ipynb		compartment-wise-LSA-calculate-intergenotype-distances.ipynb
compartment-wise-LSA-cdk-wt-sh-batch-stats-analysis.ipynb		compartment-wise-LSA-cdk-wt-sh-batch-stats-analysis.ipynb
compartment-wise-LSA-mitosispattern-studies.ipynb		compartment-wise-LSA-mitosispattern-studies.ipynb
compartment-wise-LSA-wing-batch-stats-MASKANALYSIS.ipynb		compartment-wise-LSA-wing-batch-stats-MASKANALYSIS.ipynb
compartment-wise-SH-SEPARATEDCOMPARTMENTS-batch-stats-analysis.ipynb		compartment-wise-SH-SEPARATEDCOMPARTMENTS-batch-stats-analysis.ipynb
compartment-wise-SH-wing-batch-stats-PCAMASKANALYSIS.ipynb		compartment-wise-SH-wing-batch-stats-PCAMASKANALYSIS.ipynb
compartment-wise-WT-SEPARATEDCOMPARTMENTS-batch-stats-analysis.ipynb		compartment-wise-WT-SEPARATEDCOMPARTMENTS-batch-stats-analysis.ipynb
compartment-wise-WT-wing-batch-stats-PCAMASKANALYSIS.ipynb		compartment-wise-WT-wing-batch-stats-PCAMASKANALYSIS.ipynb
compartment-wise-add-star-align-parameters-to-WEA.ipynb		compartment-wise-add-star-align-parameters-to-WEA.ipynb
compartment-wise-generate-smooth-SAF-and-MASK-dev.ipynb		compartment-wise-generate-smooth-SAF-and-MASK-dev.ipynb
compartment-wise-linearshearalignment-batch-analysis.ipynb		compartment-wise-linearshearalignment-batch-analysis.ipynb
compartment-wise-procrustes-alignment-SFA-batch-code-prep.ipynb		compartment-wise-procrustes-alignment-SFA-batch-code-prep.ipynb
compartment-wise-procrustes-alignment-SFA-tomer-advice.ipynb		compartment-wise-procrustes-alignment-SFA-tomer-advice.ipynb
compartment_analyzer.py		compartment_analyzer.py
convert_wrl_to_ply.py		convert_wrl_to_ply.py
dans_fourier_high_pass_edge_filter_roi_load.ipynb		dans_fourier_high_pass_edge_filter_roi_load.ipynb
first_pass_at_cell_size_histograms.ipynb		first_pass_at_cell_size_histograms.ipynb
fly_wing_curvature_PLANE_FITTING.ipynb		fly_wing_curvature_PLANE_FITTING.ipynb
fly_wing_curvature_analysis.ipynb		fly_wing_curvature_analysis.ipynb
fullwing-procrustes-batch-analysis-PCA.ipynb		fullwing-procrustes-batch-analysis-PCA.ipynb
genotype_spread_bootstrap_analysis.py		genotype_spread_bootstrap_analysis.py
get_wings_for_Hitanshu.ipynb		get_wings_for_Hitanshu.ipynb
hitanshu_edge_code.py		hitanshu_edge_code.py
image_smoothing_toolbox.py		image_smoothing_toolbox.py
intergenotype-distance-bootstrap-analysis.py		intergenotype-distance-bootstrap-analysis.py
intergenotype-tpe-difference-notebook.ipynb		intergenotype-tpe-difference-notebook.ipynb
intro_to_boundary_detection.ipynb		intro_to_boundary_detection.ipynb
manual-correction.ipynb		manual-correction.ipynb
network-polygon-analysis-of-different-adjacency-matrices.ipynb		network-polygon-analysis-of-different-adjacency-matrices.ipynb
network_polygons.py		network_polygons.py
post-tree-FRANKENSTEIN-spatial-stats-fields.ipynb		post-tree-FRANKENSTEIN-spatial-stats-fields.ipynb
preprocessing_SH_dev_without_R_and_L_in_name.ipynb		preprocessing_SH_dev_without_R_and_L_in_name.ipynb
process_voronoi.py		process_voronoi.py
procrustes.ipynb		procrustes.ipynb
procrustes_alignment_testing.ipynb		procrustes_alignment_testing.ipynb
readme_AVERAGEPATTERNDDIFFERENCE.docx		readme_AVERAGEPATTERNDDIFFERENCE.docx
readme_AVERAGEPATTERNDDIFFERENCE.txt		readme_AVERAGEPATTERNDDIFFERENCE.txt
readme_Bootstrap.docx		readme_Bootstrap.docx
readme_Bootstrap.txt		readme_Bootstrap.txt
ridge-removal-dev.ipynb		ridge-removal-dev.ipynb
rigid_body_shapely_analysis_for_MarchMeeting.ipynb		rigid_body_shapely_analysis_for_MarchMeeting.ipynb
script_TO_CALC_SM_FROM_CPP.py		script_TO_CALC_SM_FROM_CPP.py

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FlyAnalysis: this is a replacement for the Mondal_first_pass branch of Dan McCusker's bristlepipelines repo. We overfilled that repo with data and it appears to be unfixable.

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