LICENSE.md
README.md
setup.py
coppafish/__init__.py
coppafish/__main__.py
coppafish/_version.py
coppafish.egg-info/PKG-INFO
coppafish.egg-info/SOURCES.txt
coppafish.egg-info/dependency_links.txt
coppafish.egg-info/requires.txt
coppafish.egg-info/top_level.txt
coppafish/call_spots/__init__.py
coppafish/call_spots/background.py
coppafish/call_spots/background_optimised.py
coppafish/call_spots/base.py
coppafish/call_spots/bleed_matrix.py
coppafish/call_spots/dot_product.py
coppafish/call_spots/dot_product_optimised.py
coppafish/call_spots/qual_check.py
coppafish/call_spots/qual_check_optimised.py
coppafish/call_spots/test/__init__.py
coppafish/call_spots/test/test_base.py
coppafish/call_spots/test/test_bleed_matrix.py
coppafish/call_spots/test/test_optimised.py
coppafish/extract/__init__.py
coppafish/extract/base.py
coppafish/extract/deconvolution.py
coppafish/extract/fstack.py
coppafish/extract/scale.py
coppafish/extract/test/__init__.py
coppafish/extract/test/test_fstack.py
coppafish/extract/test/test_strip_hack.py
coppafish/find_spots/__init__.py
coppafish/find_spots/base.py
coppafish/find_spots/check_spots.py
coppafish/find_spots/detect.py
coppafish/find_spots/detect_optimised.py
coppafish/find_spots/test/__init__.py
coppafish/find_spots/test/random_spot.py
coppafish/find_spots/test/test_base.py
coppafish/find_spots/test/test_neighbour.py
coppafish/find_spots/test/test_optimised.py
coppafish/omp/__init__.py
coppafish/omp/base.py
coppafish/omp/coefs.py
coppafish/omp/coefs_optimised.py
coppafish/omp/spots.py
coppafish/omp/test/__init__.py
coppafish/omp/test/test_all.py
coppafish/omp/test/test_optimised.py
coppafish/pipeline/__init__.py
coppafish/pipeline/basic_info.py
coppafish/pipeline/call_reference_spots.py
coppafish/pipeline/extract_run.py
coppafish/pipeline/find_spots.py
coppafish/pipeline/get_reference_spots.py
coppafish/pipeline/omp.py
coppafish/pipeline/register.py
coppafish/pipeline/register_initial.py
coppafish/pipeline/run.py
coppafish/pipeline/stitch.py
coppafish/plot/__init__.py
coppafish/plot/raw.py
coppafish/plot/call_spots/__init__.py
coppafish/plot/call_spots/background.py
coppafish/plot/call_spots/bleed_matrix.py
coppafish/plot/call_spots/dot_product.py
coppafish/plot/call_spots/gene_counts.py
coppafish/plot/call_spots/scaled_k_means.py
coppafish/plot/call_spots/score_calc.py
coppafish/plot/call_spots/spot_colors.py
coppafish/plot/call_spots/weight.py
coppafish/plot/extract/__init__.py
coppafish/plot/extract/diagnostics.py
coppafish/plot/extract/viewer.py
coppafish/plot/find_spots/__init__.py
coppafish/plot/find_spots/n_spots.py
coppafish/plot/find_spots/viewer.py
coppafish/plot/omp/__init__.py
coppafish/plot/omp/coefs.py
coppafish/plot/omp/score_hist.py
coppafish/plot/omp/score_shape.py
coppafish/plot/omp/track_fit.py
coppafish/plot/register/__init__.py
coppafish/plot/register/diagnostics.py
coppafish/plot/register/icp.py
coppafish/plot/register/shift.py
coppafish/plot/results_viewer/__init__.py
coppafish/plot/results_viewer/base.py
coppafish/plot/results_viewer/cellClassColors.json
coppafish/plot/results_viewer/cell_color.csv
coppafish/plot/results_viewer/gene_color.csv
coppafish/plot/results_viewer/legend.py
coppafish/plot/stitch/__init__.py
coppafish/plot/stitch/diagnostics.py
coppafish/plot/stitch/point_clouds.py
coppafish/plot/stitch/shift.py
coppafish/register/__init__.py
coppafish/register/base.py
coppafish/register/check_transforms.py
coppafish/register/test/__init__.py
coppafish/register/test/test_base.py
coppafish/setup/__init__.py
coppafish/setup/config.py
coppafish/setup/dye_camera_laser_raw_intensity.csv
coppafish/setup/file_names.py
coppafish/setup/notebook.py
coppafish/setup/notebook_comments.json
coppafish/setup/settings.default.ini
coppafish/setup/tile_details.py
coppafish/setup/test/__init__.py
coppafish/setup/test/test_config.py
coppafish/setup/test/test_notebook.py
coppafish/setup/test/test_tilepos.py
coppafish/spot_colors/__init__.py
coppafish/spot_colors/base.py
coppafish/spot_colors/base_optimised.py
coppafish/spot_colors/test/__init__.py
coppafish/spot_colors/test/data_initialise.py
coppafish/spot_colors/test/test_spot_colors.py
coppafish/stitch/__init__.py
coppafish/stitch/check_shifts.py
coppafish/stitch/shift.py
coppafish/stitch/starting_shifts.py
coppafish/stitch/tile_origin.py
coppafish/stitch/test/__init__.py
coppafish/stitch/test/test_shift.py
coppafish/stitch/test/test_tile_origin.py
coppafish/utils/__init__.py
coppafish/utils/base.py
coppafish/utils/errors.py
coppafish/utils/matlab.py
coppafish/utils/nd2.py
coppafish/utils/npy.py
coppafish/utils/pciseq.py
coppafish/utils/raw.py
coppafish/utils/spot_images.py
coppafish/utils/strel.py
coppafish/utils/warnings.py
coppafish/utils/morphology/__init__.py
coppafish/utils/morphology/base.py
coppafish/utils/morphology/filter.py
coppafish/utils/morphology/filter_optimised.py
coppafish/utils/test/__init__.py
coppafish/utils/test/test_morphology.py
coppafish/utils/test/test_npy.py
coppafish/utils/test/test_optimised.py