.travis.yml
AUTHORS
AUTHORS.rst
ChangeLog
LICENSE
README.rst
appveyor.yml
readthedocs-requirements.txt
requirements.txt
setup.cfg
setup.py
colicoords/__init__.py
colicoords/cell.py
colicoords/config.py
colicoords/data_models.py
colicoords/fileIO.py
colicoords/fitting.py
colicoords/iplot.py
colicoords/minimizers.py
colicoords/models.py
colicoords/plot.py
colicoords/postprocess.py
colicoords/preprocess.py
colicoords/support.py
colicoords/synthetic_data.py
colicoords.egg-info/PKG-INFO
colicoords.egg-info/SOURCES.txt
colicoords.egg-info/dependency_links.txt
colicoords.egg-info/not-zip-safe
colicoords.egg-info/pbr.json
colicoords.egg-info/requires.txt
colicoords.egg-info/top_level.txt
colicoords/cnn/LICENSE.md
colicoords/cnn/losses.py
colicoords/cnn/preprocess.py
colicoords/cnn/unet.py
colicoords/gui/__init__.py
colicoords/gui/controller.py
colicoords/gui/images_select.py
docs/advanced_usage.rst
docs/align_cells.rst
docs/batch_processing.rst
docs/conf.py
docs/configuration.rst
docs/coords.rst
docs/index.rst
docs/indexing.rst
docs/installation.rst
docs/introduction.rst
docs/modules.rst
docs/optimization.rst
docs/refs.bib
docs/storm_data.rst
docs/figures/batch_processing_properties.png
docs/figures/batch_processing_r_dist.png
docs/figures/bf_coords_only.png
docs/figures/introduction_cell_images.png
docs/figures/introduction_coordinates_final.png
docs/figures/introduction_coordinates_initial.png
docs/figures/introduction_flu_rdist.png
examples/01_basic_usage.ipynb
examples/02_batch_processing.ipynb
examples/03_coordinate_system_optimization.ipynb
examples/04_coordinate_transform_and_cell_alignment.ipynb
examples/05_exploring_data_and_indexing.ipynb
examples/CNN_01_training_neural_networks.ipynb
examples/CNN_02_applying_neural_networks.ipynb
examples/data/01_binary.tif
examples/data/01_brightfield.tif
examples/data/01_fluorescence.tif
examples/data/02_binary_stack.tif
examples/data/02_brightfield_stack.tif
examples/data/02_fluorescence_stack.tif
examples/data/03_synthetic_cells.hdf5
examples/data/05_synthetic_foci.hdf5
images/ColiCoords_Final_Full.svg
images/ColiCoords_Final_Icon.svg
images/ColiCoords_Final_Logo.svg
images/ColiCoords_Final_Screen.svg
images/pipeline_figure.png
images/pipeline_figure.svg
test/__init__.py
test/test_basic_functions.py
test/test_cell.py
test/test_data_models.py
test/test_fileio.py
test/test_fitting.py
test/test_functions.py
test/test_preprocessing.py
test/test_rdist_fitting.py
test/test_support.py
test/test_synthetic_data.py
test/testcase.py
test/test_data/test_cells.hdf5
test/test_data/test_double_spot_storm.hdf5
test/test_data/test_single_spot_storm.hdf5
test/test_data/test_synth_cell_storm.hdf5
test/test_data/ds1/binary/00001_Probabilities_filtered.tif
test/test_data/ds1/binary/00002_Probabilities_filtered.tif
test/test_data/ds1/binary/00003_Probabilities_filtered.tif
test/test_data/ds1/binary/00004_Probabilities_filtered.tif
test/test_data/ds1/binary/00005_Probabilities_filtered.tif
test/test_data/ds1/binary/00006_Probabilities_filtered.tif
test/test_data/ds1/binary/00007_Probabilities_filtered.tif
test/test_data/ds1/binary/00008_Probabilities_filtered.tif
test/test_data/ds1/binary/00009_Probabilities_filtered.tif
test/test_data/ds1/binary/00010_Probabilities_filtered.tif
test/test_data/ds1/brightfield/00001.tif
test/test_data/ds1/brightfield/00002.tif
test/test_data/ds1/brightfield/00003.tif
test/test_data/ds1/brightfield/00004.tif
test/test_data/ds1/brightfield/00005.tif
test/test_data/ds1/brightfield/00006.tif
test/test_data/ds1/brightfield/00007.tif
test/test_data/ds1/brightfield/00008.tif
test/test_data/ds1/brightfield/00009.tif
test/test_data/ds1/brightfield/00010.tif
test/test_data/ds1/fluorescence/00001.tif
test/test_data/ds1/fluorescence/00002.tif
test/test_data/ds1/fluorescence/00003.tif
test/test_data/ds1/fluorescence/00004.tif
test/test_data/ds1/fluorescence/00005.tif
test/test_data/ds1/fluorescence/00006.tif
test/test_data/ds1/fluorescence/00007.tif
test/test_data/ds1/fluorescence/00008.tif
test/test_data/ds1/fluorescence/00009.tif
test/test_data/ds1/fluorescence/00010.tif
test/test_data/ds2/data_src.txt
test/test_data/ds2/binary/00066_Probabilities_filtered.tif
test/test_data/ds2/binary/00074_Probabilities_filtered.tif
test/test_data/ds2/brightfield/00066.tif
test/test_data/ds2/brightfield/00074.tif
test/test_data/ds2/fluorescence/00066.tif
test/test_data/ds2/fluorescence/00074.tif
test/test_data/ds3/binary.tif
test/test_data/ds3/flu.tif
test/test_data/ds3/storm_table.csv