Add a Quick Start tutorial #1869
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neuromusic
approved these changes
Apr 14, 2020
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| from starfish import data | ||
| from starfish.image import Filter | ||
| from starfish.image import ApplyTransform, LearnTransform | ||
| from starfish.spots import FindSpots, DecodeSpots | ||
| from starfish.types import Features, Axes | ||
| from starfish.image import Segment | ||
| from starfish.spots import AssignTargets | ||
| from starfish import ExpressionMatrix | ||
| from starfish import ImageStack | ||
|
|
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| import numpy as np | ||
| import matplotlib.pyplot as plt | ||
| import pandas as pd | ||
| import seaborn as sns |
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for tutorials, I prefer to do imports in the same block that they are used. a large list of imports is likely to be glanced over. keeping the imports in the same block where they are used lets the user understand where each processing step lives.
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| 'capture_repr': ('_repr_html_', '__repr__'), | ||
| 'ignore_repr_types':r'str|matplotlib.axes', |
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| # set subsection order | ||
| 'subsection_order': ExplicitOrder(['../../examples/quick_start', | ||
| '../../examples', | ||
| '../../examples/data_formatting', | ||
| '../../examples/data_loading', | ||
| '../../examples/how_to', | ||
| '../../examples/pipelines', | ||
| ]), |
Codecov Report
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## master #1869 +/- ##
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Coverage 87.77% 87.77%
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Files 168 168
Lines 5785 5785
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Hits 5078 5078
Misses 707 707 Continue to review full report at Codecov.
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See it on read the docs here.
The Quick Start tutorial is aimed at introducing new users unfamiliar with starfish to all the basic components of a starfish pipeline in under 10 minutes. It allows them to "demo" starfish and hopefully entices them to try using starfish to process their own data.
List of changes: