big-fish 0.6.2

Version 0.6.2:

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

big-fish 0.6.1

Version 0.6.1:

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)

big-fish 0.6

Version 0.6:

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)

big-fish 0.5

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)

big-fish 0.4

Version 0.4:

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)

big-fish 0.3

Version 0.3:

• 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.

big-fish 0.2

Version used for the 2020 QBI poster Feature representations for the identification of mRNA localization patterns from smFISH data.

big-fish 0.1

Version used for the paper A dual protein/mRNA localization screen reveals compartmentalized translation and widespread co-translational RNA targeting, Chouaib et al. (2020).