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big-fish 0.5
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@Henley13 Henley13 released this 15 Jul 22:44
0.5
5512b6e
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Learn about vigilant mode.

Version 0.5:

Major upgrades
Add function bigfish.detection.compute_snr to compute signal-to-noise ratio (c26195e, b3a2078, 44d7b36, b753784, fabb7e2, e367a2f, ba8806a)
Add sphinx documentation (751190e, c77a08c, e26aa28, 31af14c, cfbc90e, ddd1319, 86e21ad, 22cbf0a, 7520e0d, aaa0d6a, 0f46ba1, 8ab1e39, 43b60a6, 943f537)
Refactor and reword bigfish.detection (d219373, fa0df4f)
Add deep learning models to segment nuclei and cells (a901bd8, 9ebf35e, 4dfc431, efc51ff, 37fb620, fac4a75)
Add function bigfish.plot. plot_elbow to plot the elbow curve (3e47346, 76ec306)
Add function bigfish.detection.fit_subpixel to perform subpixel spot detection (ddab584)

Minor upgrades
Move get_sigma and get_radius in bigfish.stack (1827749)
Remove outdated functions and modules (2607f36)
Make bigfish.stack.mean_filter faster (13b4ce8)
Allow float image for bigfish.stack.mean_filter (6ad1eec)
Refactor functions for focus projection and measure (0e23bfe)
Allow float spot coordinates for bigfish.plot.plot_detection (6613f11)
Add parameter in bigfish.detection.decompose_dense to manage the denoising filter (4766885)
Remove original version of focus projection (b9d1afc)
Add warning when no spot is detected (5ee4e7a)
Update setup.py (6fd8e84, 9a9cf2b)
Add functions to count segmented instance and compute their diameter (8847fb4)
Add function bigfish.stack.augment_2d_function to randomly return an image augmentation transformation (eea2c35)
Change default frame size in bigfish.plot (e9596e3)
Add function bigfish.plot.plot_segmentation_diff to compare segmented instance with their ground truth (2545457, 0f18d9b)
Improve postprocessing functions in bigfish.segmentation and nucleus-cell matching (1298f1b, dcd9c1c)
Add function bigfish.stack.augment_8_times to apply every augmentation transformation to an image(e3932ca, 6795748)
Make some functions public to be imported from external packages (e1c104e, f544f2e)
Update loader functions to get new images for example (6115694)
Remove a former module used for pattern classification (2b8ebaa)
Update README (be21078)
Update requirement_dev.txt (39faf85)

Bug fixes
Fix bug with float voxel_size in bigfish.detection (b9776d5)
Fix bug in bigfish.plot.plot_images (b3a47d3)

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