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Project: starfish
(GitHub Link)
starfish-master
.github
ISSUE_TEMPLATE
user-story.md
feature_request.md
bug_report.md
Makefile
.travis-config.json
examples
data_formatting
README.txt
plot_format_tilefetcher.py
plot_format_structured_data.py
how_to
assess_spotfindingresults.py
metric_distance.py
clip.py
trackpy_local_max_peak_finder.py
README.txt
plot_display.py
match_histograms.py
clip_percentile_to_zero.py
tracebuildingstrategies.py
clip_value_to_zero.py
imshow_plane.py
simple_lookup_decoder.py
per_round_max_channel.py
blob_detector.py
local_max_peak_finder.py
intensity_histogram.py
README.txt
tutorials
normalize_intensity_values.py
plot_image_manipulations.py
plot_image_registration.py
watershed_segmentation.py
assigning_spots.py
spotbased_decoding.py
pixelbased_decoding.py
manual_segmentation.py
README.txt
plot_illumination_correction.py
run_ilastik.sh
ilastik_segmentation.py
transforms_list.json
normalize_intensity_distributions.py
plot_tissue_specific_corrections.py
pipelines
3d_smFISH.py
iss_pipeline.py
README.txt
subdir.mk
quick_start
README.txt
plot_quick_start.py
data_loading
plot_tilefetcher_loader.py
README.txt
plot_loading_data.py
data_formatting_examples
format_iss_data.py
format_merfish_U2OS_data.py
format_osmfish.py
format_iss_breast_data.py
format_starmap.py
README.txt
format_seqFISH.py
format_imc_data.py
format_baristaseq.py
readthedocs.yml
starfish
data.py
spacetx_format
examples
field_of_view
coordinates_good_max.json
coordinates_bad_z_single.json
coordinates_bad_z_triple.json
coordinates_bad_x_scalar.json
coordinates_good_min.json
coordinates_bad_y_scalar.json
dartfish_field_of_view.json
too_large.json
coordinates_bad_y_single.json
field_of_view.json
dartfish_nuclei.json
coordinates_bad_x_single.json
codebook
codebook.json
codebook_diagonal_inferred_value.json
codebook_diagonal.json
fov_manifest
fov_manifest.json
experiment
experiment.json
dartfish_experiment.json
no_fov_manifest.json
README.md
schema
field_of_view_0.1.0
tiles
coordinates.json
indices.json
tiles.json
field_of_view.json
experiment_5.0.0.json
fov_manifest_0.0.0.json
extras.json
field_of_view_0.0.0
tiles
coordinates.json
indices.json
tiles.json
field_of_view.json
README.md
codebook_0.0.0
codebook.json
codeword.json
experiment_4.0.0.json
fov_manifest_0.1.0.json
version.json
image.py
config.py
morphology.py
test
full_pipelines
api
test_merfish.py
test_iss_doc_pipeline.py
test_dartfish.py
__init__.py
test_allen_smFISH.py
test_iss_api.py
__init__.py
__init__.py
util
plot.py
__init__.py
__main__.py
__init__.py
core
_display.py
spots
DetectPixels
test
test_targets_map.py
test_create_spot_attributes.py
test_intensities_to_decoded_image.py
__init__.py
test_calculate_mean_pixel_traces.py
__init__.py
_base.py
combine_adjacent_features.py
pixel_spot_decoder.py
AssignTargets
label.py
__init__.py
_base.py
DecodeSpots
metric_decoder.py
trace_builders.py
util.py
test
test_composite_codebook.py
test_spot_finders.py
test_metric_decoder.py
test_decoding_without_spots.py
test_trace_builders.py
__init__.py
test_nearest_neighbor_trace_builder.py
per_round_max_channel_decoder.py
__init__.py
simple_lookup_decoder.py
_base.py
__init__.py
FindSpots
spot_finding_utils.py
blob.py
test
test_synthetic_data.py
test_spot_detection.py
test_local_max_peak_finder.py
__init__.py
trackpy_local_max_peak_finder.py
__init__.py
_base.py
local_max_peak_finder.py
spacetx_format
test_codebook.py
util.py
test_coordinates.py
test_fuzz.py
cli.py
test_experiment.py
validate_sptx.py
test
test_validate.py
test_fov_manifest.py
test_field_of_view.py
__init__.py
starfish.py
expression_matrix
test
test_serialization.py
__init__.py
test_concatenate.py
concatenate.py
expression_matrix.py
__init__.py
test
factories.py
test_synthetic_spot_creation.py
test_display.py
test_multiprocessing_workflow.py
__init__.py
util
exec.py
click
__init__.py
config.py
test
test_preserve_float_range.py
test_levels.py
__init__.py
levels.py
try_import.py
clock.py
__init__.py
logging.py
argparse.py
enum.py
codebook
test
test_approximate_nearest_code.py
test_synthetic_one_hot_codebook.py
factories.py
test_code_length.py
test_to_json.py
test_metric_decode.py
test_per_round_max_decode.py
__init__.py
test_normalize_code_traces.py
test_from_code_array.py
__init__.py
_format.py
codebook.py
config
test
test_config.py
__init__.py
__init__.py
intensity_table
overlap.py
test
test_stack_intensity_table_reshaping.py
factories.py
test_from_imagestack.py
test_intensity_table_serialization.py
test_empty_intensity_table.py
test_overlap.py
__init__.py
test_synthetic_intensities.py
test_concatenate.py
test_to_mermaid.py
test_from_spot_data.py
test_intensity_table_coords.py
decoded_intensity_table.py
concatenate.py
__init__.py
intensity_table.py
intensity_table_coordinates.py
types
_spot_finding_results.py
_validated_table.py
_spot_attributes.py
_functionsource.py
test
test_decoded_spots.py
__init__.py
__init__.py
_constants.py
_decoded_spots.py
segmentation_mask
segmentation_mask.py
__init__.py
__init__.py
_version.py
errors.py
experiment
builder
providers.py
structured_formatter.py
test
test_inplace.py
test_small_axis.py
structured_formatter
test_single_fov.py
util.py
test_tilepath.py
__init__.py
test_multiple_fov.py
__init__.py
test_orderediterator.py
factories
all_purpose.py
__init__.py
unique_tiles.py
defaultproviders.py
__init__.py
inplace.py
orderediterator.py
builder.py
version.py
test
test_experiment.py
test_version.py
__init__.py
experiment.py
__init__.py
pipeline
algorithmbase.py
__init__.py
imagestack
physical_coordinates.py
imagestack.py
test
test_labeled_indices.py
test_from_tilefetcher.py
test_apply.py
test_metadata.py
test_coordinates.py
test_physical_coordinate_calculator.py
test_slicedimage_dtype.py
test_index.py
test_max_proj.py
test_from_numpy_array.py
imagestack_test_utils.py
__init__.py
test_slice_ops.py
test_cropped_load.py
factories
with_coords.py
all_purpose.py
synthetic_stack.py
__init__.py
from_codebook.py
unique_tiles.py
test_export.py
dataorder.py
indexing_utils.py
__init__.py
parser
_tiledata.py
tileset
_parser.py
__init__.py
_key.py
crop.py
numpy
__init__.py
__init__.py
tilefetcher
_parser.py
__init__.py
compat.py
image
_registration
test
test_transforms_list.py
__init__.py
transforms_list.py
LearnTransform
test
test_translation.py
__init__.py
translation.py
__init__.py
_base.py
__init__.py
ApplyTransform
test
__init__.py
test_warp.py
__init__.py
warp.py
_base.py
_format.py
Filter
linear_unmixing.py
element_wise_mult.py
util.py
gaussian_low_pass.py
zero_by_channel_magnitude.py
ilastik_pre_trained_probability.py
clip.py
test
test_white_tophat.py
test_api_contract.py
test_histogram_matching.py
test_reduce.py
test_linear_unmixing.py
test_call_bases.py
test_zero_by_channel_magnitude.py
test_map.py
__init__.py
test_filter.py
richardson_lucy_deconvolution.py
gaussian_high_pass.py
match_histograms.py
clip_percentile_to_zero.py
bandpass.py
clip_value_to_zero.py
call_bases.py
laplace.py
__init__.py
white_tophat.py
mean_high_pass.py
_base.py
map.py
reduce.py
Segment
__init__.py
_base.py
watershed.py
__init__.py
morphology
Merge
simple.py
test
test_simple.py
__init__.py
__init__.py
_base.py
util.py
label_image
test
test_label_image.py
__init__.py
label_image.py
__init__.py
binary_mask
test
test_from_binary_arrays_and_ticks.py
factories.py
test_binary_mask.py
test_expand.py
test_from_label_array_and_ticks.py
__init__.py
expand.py
binary_mask.py
__init__.py
_io.py
Filter
min_distance_label.py
test
test_areafilter.py
test_reduce.py
test_map.py
__init__.py
areafilter.py
__init__.py
_base.py
map.py
reduce.py
structural_label.py
Binarize
test
__init__.py
test_threshold.py
threshold.py
__init__.py
_base.py
Segment
__init__.py
_base.py
watershed.py
__init__.py
experiment
__init__.py
builder.py
test.py
types.py
REQUIREMENTS-STRICT.txt
spots.py
codecov.yml
LICENSE
versioneer.py
.flake8
.gitattributes
paper
paper.md
paper.bib
CHANGELOG.md
README.rst
notebooks
BaristaSeq.ipynb
MERFISH.ipynb
ISS.ipynb
DARTFISH.ipynb
STARmap.ipynb
osmFISH.ipynb
data
SeqFISH.ipynb
py
BaristaSeq.py
MERFISH.py
ISS.py
smFISH.py
SeqFISH.py.skip
README.txt
Starfish_simulation.py.skip
STARmap.py.skip
data
osmFISH.py
STARmap.py
SeqFISH.py
DARTFISH.py
Starfish_simulation.py
smFISH.ipynb
subdir.mk
Starfish_simulation.ipynb
setup.py
docker
Dockerfile
REQUIREMENTS.txt
setup.cfg
workflows
wdl
starfish.wdl
iss_published
recipe.py
inputs.json
test_inputs.json
merfish_published
recipe.py
inputs.json
test_inputs.json
iss_spaceTX
recipe.py
inputs.json
test_inputs.json
.travis.yml
CONTRIBUTING.rst
.hgtags
.gitignore
docs
Makefile
source
help_and_reference
configuration
index.rst
spacetx_consortium
index.rst
usage
index.rst
data_model
index.rst
glossary
glossary.rst
processing_at_scale
index.rst
working_with_starfish_outputs
IntensityTable
index.rst
DecodedSpots
index.rst
SegmentationMask
index.rst
index.rst
ExpressionMatrix
index.rst
request_support
index.rst
available_datasets
index.rst
spacetx-format
SpaceTxFormat
index.rst
index.rst
Validation
index.rst
index.rst
about
index.rst
api
spots
index.rst
datasets
index.rst
utils
logging.rst
config.rst
index.rst
experiment_builder
index.rst
data_structures
intensity_table.rst
expression_matrix.rst
binary_mask.rst
experiment.rst
codebook.rst
image_stack.rst
decoded_intensity_table.rst
field_of_view.rst
index.rst
label_image.rst
display
index.rst
slicedimage
index.rst
types
index.rst
validation
index.rst
index.rst
image
index.rst
plot_utils
index.rst
morphology
index.rst
developer_guide
index.rst
index.rst
conf.py
_templates
layout.html
relations.html
_static
example_data_files
README.rst
images
design
README
favicon.ico
my-styles.css
installation
index.rst
user_guide
index.rst
.dockerignore
requirements
REQUIREMENTS-NAPARI-CI.txt
REQUIREMENTS-NAPARI-CI.txt.in
REQUIREMENTS-CI.txt
REQUIREMENTS-CI.txt.in
MANIFEST.in