Big-fish

**Major upgrades**

**Minor upgrades**
Add a Readme for the documentation folder (1ab69fc)
Update versions in requirements (1879853)
Allow saving of 1D array (09259cb)
Add function to plot coordinates representation of several cells at once (2dbb86a)
Allow integer 32-bit as input for several functions (8fe67e0, 1882b6c, e936898, 9530223)
Add cell and nucleus areas as default results extracted (1da7273)
Make function to extract spot volume and surface public (8032791)

**Bug fixes**

**Major upgrades**
Unpin dependencies (9b7f1d5, da4c646, d091215, 384c144, a8172b5)

**Minor upgrades**
Improve docstring (39c041a)
Add badge with different Python versions in the Readme (f2b5af4, 4886b4c)
Update codecov configuration file (da4d4ef)
Add unit tests in `bigfish.stack` (45355fb)
Add 'delimiter' parameter in `bigfish.multistack.summarize_extraction_results` (a0a2a8e)
Add 'skiprows' parameter in `bigfish.stack.read_array_from_csv` (c635e0f)
Add a parameter to set boundaries width in segmentation plots (b926489)
Add citation in Readme and documentation (2047ebf)

**Bug fixes**
Fix side bar alignment in documentation (2b3af3f)
Fix bug in `bigfish.stack.compute_focus` (0a08a3f)
Fix bug in `bigfish.stack.focus_projection` to not define null voxels as out-of-focus voxels (86de38b)

**Major upgrades**
Add new subpackage bigfish.multistack to gather different postprocessing functions (8ee7e55, dc1b0e0, ab3a531, 8a075d2, ede24a7, e3bc675, 5041600, 1f96b80, 398de7f)
Add function to plots and detect colocalized spots (eeb3256)
Remove mention of PSF from the package and update the input arguments in several bigfish.detection functions (35e5433, 2b26fcb, 609d332)


**Minor upgrades**
Remove illumination module in bigfish.stack (999de09)
Add unitary test for augmentation module in bigfish.stack (999de09)
Change 'cyt' to 'cell' (eef0848)
Add a build script in bash (a24a9fa)

**Major upgrades**
Add function `bigfish.detection.compute_snr` to compute signal-to-noise ratio (c26195e7bb774077ed2394a04cfffb3cbc0f4ce6, b3a20783dbb448460e427e5828a38fb6792f2a49, 44d7b367a9305048a56cb6255bccd3bea03893f7, b753784d7d29bd6dde0a96cf4789a65bb1a4ef22, fabb7e2653de183c3b0dd9e168ddde58c0563a2e, e367a2f0e25a0e34b82714b7fb562b05549b9e53, ba8806aa232b3b0d95257af413c0879d165b13f6)
Add sphinx documentation (751190e44e092a9f9466ff19bfd1fce79876039a, c77a08c0430b47bb403a952f823ca17c60e8e168, e26aa28aab4821cb9752036d3ca5b073be760b95, 31af14c0675006523e3c66bc80030a36c5091c49, cfbc90e0182fb24e4eacd5cae36fb0dcff692827, ddd131968357ca23cbed974a82762026911e1fd8, 86e21adb70d5f663e6107f9d31529da7c07017ac, 22cbf0a7b40d6b4c71577cf291ded012fecbaaea, 7520e0d55f2ad9265fd4dffd87bdf358ebf6a456, aaa0d6a590ec85af1c0d5170bc3e3c3c7d6969ab, 0f46ba10153db7074ffdda01ad5ae1947d3ccd1a, 8ab1e39d646e404585e94ce147e8c4f1e66dba36, 43b60a6e448d50659ee1274d5d466fc568137638, 943f53762c3d0179fca4984f6cf156701e128113)
Refactor and reword `bigfish.detection` (d219373c0c0ab2670c21eac2ec33ab39157d3d2e, fa0df4fdd10656e6c87371c22fefa4fef43de3df)
Add deep learning models to segment nuclei and cells (a901bd8f0d91641313be0aeb72bfa7d24ee0207a, 9ebf35ef5c182355a757a46ec5c81b49ab1c1233, 4dfc43196fa5ecb2d02dc2e407427f83a7623372, efc51ffb4719378b9ce189f6d7ec709a9ff5d448, 37fb620bfabf57a2c96bc22a6c0f4c124269795d, fac4a75c54fb4628b5e37b487b23fc90a521f3ba)
Add function `bigfish.plot. plot_elbow` to plot the elbow curve (3e47346322aff05346e793c4fa0829ddad50b687, 76ec30604a4014a6bfa06d1a6f107a5c32fd86f9)
Add function `bigfish.detection.fit_subpixel` to perform subpixel spot detection (ddab58446bc4ab2726a9426d53da0338cafa90fb)

**Minor upgrades**
Move `get_sigma` and `get_radius` in `bigfish.stack` (1827749eded9341d1e5563b94046b0b859b7d6fb)
Remove outdated functions and modules (2607f36a8f007dbc41421d2b1296ac55e385a06b)
Make `bigfish.stack.mean_filter` faster (13b4ce8b8aabee0cc783161c61f96077fb58fc7b)
Allow float image for `bigfish.stack.mean_filter` (6ad1eecce45609783af94f0b96545872ef098288)
Refactor functions for focus projection and measure (0e23bfec08df438689d38c530aaea718946c2442)
Allow float spot coordinates for `bigfish.plot.plot_detection` (6613f1105c8d88b1c0745283d911b24cb45a08ee)
Add parameter in `bigfish.detection.decompose_dense` to manage the denoising filter (4766885e1de26d09d2c8c58f3dd9427924c87173)
Remove original version of focus projection (b9d1afcc881f68a3160ba76a2c23ec7bed5bd836)
Add warning when no spot is detected (5ee4e7a2dab52f94870358b1d1e99a141d633c5f)
Update `setup.py` (6fd8e845bb513fed354a98e916127aa43eeef3ab, 9a9cf2bef0ae4c74344b49deba39c52e9e154eb2)
Add functions to count segmented instance and compute their diameter (8847fb4b281ce84a9f898ddc0701fd8106b3d0f3)
Add function `bigfish.stack.augment_2d_function` to randomly return an image augmentation transformation (eea2c3557fde80b83a311fe087ccb8a998597250)
Change default frame size in `bigfish.plot` (e9596e3080b3652a5befc509697bc0d4befa3c23)
Add function `bigfish.plot.plot_segmentation_diff` to compare segmented instance with their ground truth (2545457ec80878ed3bd6b464b4f333b0fb505c21, 0f18d9bf62838962054955341fbe74f4e53449b2)
Improve postprocessing functions in `bigfish.segmentation` and nucleus-cell matching (1298f1bdfc8e353bba106ac32c751afdb9e916df, dcd9c1c43a0c70040f3c38416ec21572ed095d4c)
Add function `bigfish.stack.augment_8_times` to apply every augmentation transformation to an image(e3932ca954257539a6b7d7ef06fedbbfeb21a35d, 6795748a31801404663ffb97692005a9b1cad614)
Make some functions public to be imported from external packages (e1c104e690fd15a9ee1605c27353bae4a2f68e2d, f544f2e49002d99a4a1509e565c9fd19b5f473ff)
Update loader functions to get new images for example (611569419bc65e82b0870fad5830b3c144395a50)
Remove a former module used for pattern classification (2b8ebaa611170b62be1db0b2b6034a5faa43dcc6)
Update README (be21078d1fe2cb3a28e473268bc1fc5deff3bc40)
Update `requirement_dev.txt` (39faf85def17b8dbcec23dedda1a254a6efc3df7)

**Bug fixes**
Fix bug with float voxel_size in `bigfish.detection` (b9776d54690e36a2d689c073012789c2fcb99e68)
Fix bug in `bigfish.plot.plot_images` (b3a47d3afbca461b7d1db83db36b31e7fd2a57f2)

**Major upgrades**
Add automated threshold setting for spot detection (69eaff1, f595466)
Add CI and unitary test coverage with travis and codecov (5989a92, 3dbaa77)
Major refactoring of subpackage `bigfish.classification` (09e9314, aba7778, 91a203e, eadcab1, 47539b4, e36c318, 94a7264, 433d2cb)
Move notebooks and examples data (c3de121, 253a1e6, 6848b70)

**Minor upgrades**
Add parameters to control the number spots and clusters in `bigfish.detection.cluster_decomposition`(61eea05, fe34a12)
Add contrast parameters in `bigfish.plot` (261bf36, 77f1f4c, 972cd7c)
Make I/O csv functions more flexible (e0f15a4)
Allow extra images and coordinates during results extraction in `bigfish.stack.extract_cell` (4d147ae)
Add cell_id in `bigfish.stack.extract_cell` outcome (7c13689)
Add functions to identify object detected in specific sub-cellular regions with `bigfish.stack.identify_objects_in_region` (542fe7a)
Refactor function `bigfish.stack.remove_transcription_site` to remove transcription sites (2480b3c)
Add function `bigfish.stack.summarize_extraction_results` to summarize extraction results in dataframe and csv (c97f55f, 553fadf)

**Bug fixes**
Fix bug in `bigfish.segmentation.match_nuc_cell` (5e06b3b)
Fix bug in `bigfish.detection.build_reference_spot` (def504a)
Remove possible duplicate coordinates for detected local maximum (490e050)
Fix bug with `bigfish.detection.cluster_decomposition` default results (d436dd4, 3d15094)
Fix dimension bug in `bigfish.plot.plot_images` (1e53812)
Fix potential bug in `bigfish.stack.gaussian_filter` for float images with values greater than 1 (6845dcd)
Fix bug in `bigfish.detection.cluster_decomposition` with negative background estimations (a3b4c1c)

- Complete Readme.md.
- Major refactoring of subpackage `bigfish.stack`.
- Major refactoring of subpackage `bigfish.plot`.
- Major refactoring of subpackage `bigfish.segmentation`.
- Major refactoring of subpackage `bigfish.detection`.
- Add examples to run with input data.
- Initiate unitary tests.