=================================================================================== astir - Automated cell identity from single-cell multiplexed imaging and proteomics ===================================================================================
|Build Status| |PyPI| |Code Style|
.. |Build Status| image:: https://travis-ci.com/camlab-bioml/astir.svg?branch=master :target: https://travis-ci.org/camlab-bioml/astir .. |Code Style| image:: https://img.shields.io/badge/code%20style-black-black :target: https://github.com/python/black .. |PyPI| image:: https://img.shields.io/badge/pypi-v2.1-orange :target: https://pypi.org/project/pypi/
astir
is a modelling framework for the assignment of cell type across a range of single-cell technologies such as Imaging Mass Cytometry (IMC). astir
is built using pytorch <https://pytorch.org/>
_ and uses recognition networks for fast minibatch stochastic variational inference.
Key applications:
.. image:: https://www.camlab.ca/img/astir.png :align: center :alt: automated single-cell pathology
Launch the interactive tutorial: |in collab| |on github|
.. |in collab| image:: https://camo.githubusercontent.com/52feade06f2fecbf006889a904d221e6a730c194/68747470733a2f2f636f6c61622e72657365617263682e676f6f676c652e636f6d2f6173736574732f636f6c61622d62616467652e737667 :target: https://colab.research.google.com/github/camlab-bioml/Astir-Vignette/blob/main/astir_tutorial.ipynb .. |on github| image:: https://img.shields.io/badge/on-github-black :target: https://github.com/camlab-bioml/Astir-Vignette
See the full documentation <https://astir.readthedocs.io/en/latest>
and check out the tutorials <https://astir.readthedocs.io/en/latest/tutorials/index.html>
.
| Jinyu Hou, Sunyun Lee, Michael Geuenich, Kieran Campbell | Lunenfeld-Tanenbaum Research Institute & University of Toronto
Bumps ipython from 7.17.0 to 8.10.0.
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release 8.10.0560ad10
DOC: Update what's new for 8.10 (#13939)7557ade
DOC: Update what's new for 8.10385d693
Merge pull request from GHSA-29gw-9793-fvw7e548ee2
Swallow potential exceptions from showtraceback() (#13934)0694b08
MAINT: mock slowest test. (#13885)8655912
MAINT: mock slowest test.a011765
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Bumps certifi from 2020.6.20 to 2022.12.7.
9e9e840
2022.12.07b81bdb2
2022.09.24939a28f
2022.09.14aca828a
2022.06.15.2de0eae1
Only use importlib.resources's new files() / Traversable API on Python ≥3.11 ...b8eb5e9
2022.06.15.147fb7ab
Fix deprecation warning on Python 3.11 (#199)b0b48e0
fixes #198 -- update link in license9d514b4
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Bumps pillow from 7.2.0 to 9.3.0.
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9.3.0
https://pillow.readthedocs.io/en/stable/releasenotes/9.3.0.html
Changes
- Initialize libtiff buffer when saving #6699 [
@radarhere
]- Limit SAMPLESPERPIXEL to avoid runtime DOS #6700 [
@wiredfool
]- Inline fname2char to fix memory leak #6329 [
@nulano
]- Fix memory leaks related to text features #6330 [
@nulano
]- Use double quotes for version check on old CPython on Windows #6695 [
@hugovk
]- GHA: replace deprecated set-output command with GITHUB_OUTPUT file #6697 [
@nulano
]- Remove backup implementation of Round for Windows platforms #6693 [
@cgohlke
]- Upload fribidi.dll to GitHub Actions #6532 [
@nulano
]- Fixed set_variation_by_name offset #6445 [
@radarhere
]- Windows build improvements #6562 [
@nulano
]- Fix malloc in _imagingft.c:font_setvaraxes #6690 [
@cgohlke
]- Only use ASCII characters in C source file #6691 [
@cgohlke
]- Release Python GIL when converting images using matrix operations #6418 [
@hmaarrfk
]- Added ExifTags enums #6630 [
@radarhere
]- Do not modify previous frame when calculating delta in PNG #6683 [
@radarhere
]- Added support for reading BMP images with RLE4 compression #6674 [
@npjg
]- Decode JPEG compressed BLP1 data in original mode #6678 [
@radarhere
]- pylint warnings #6659 [
@marksmayo
]- Added GPS TIFF tag info #6661 [
@radarhere
]- Added conversion between RGB/RGBA/RGBX and LAB #6647 [
@radarhere
]- Do not attempt normalization if mode is already normal #6644 [
@radarhere
]- Fixed seeking to an L frame in a GIF #6576 [
@radarhere
]- Consider all frames when selecting mode for PNG save_all #6610 [
@radarhere
]- Don't reassign crc on ChunkStream close #6627 [
@radarhere
]- Raise a warning if NumPy failed to raise an error during conversion #6594 [
@radarhere
]- Only read a maximum of 100 bytes at a time in IMT header #6623 [
@radarhere
]- Show all frames in ImageShow #6611 [
@radarhere
]- Allow FLI palette chunk to not be first #6626 [
@radarhere
]- If first GIF frame has transparency for RGB_ALWAYS loading strategy, use RGBA mode #6592 [
@radarhere
]- Round box position to integer when pasting embedded color #6517 [
@radarhere
]- Removed EXIF prefix when saving WebP #6582 [
@radarhere
]- Pad IM palette to 768 bytes when saving #6579 [
@radarhere
]- Added DDS BC6H reading #6449 [
@ShadelessFox
]- Added support for opening WhiteIsZero 16-bit integer TIFF images #6642 [
@JayWiz
]- Raise an error when allocating translucent color to RGB palette #6654 [
@jsbueno
]- Moved mode check outside of loops #6650 [
@radarhere
]- Added reading of TIFF child images #6569 [
@radarhere
]- Improved ImageOps palette handling #6596 [
@PososikTeam
]- Defer parsing of palette into colors #6567 [
@radarhere
]- Apply transparency to P images in ImageTk.PhotoImage #6559 [
@radarhere
]- Use rounding in ImageOps contain() and pad() #6522 [
@bibinhashley
]- Fixed GIF remapping to palette with duplicate entries #6548 [
@radarhere
]- Allow remap_palette() to return an image with less than 256 palette entries #6543 [
@radarhere
]- Corrected BMP and TGA palette size when saving #6500 [
@radarhere
]
... (truncated)
Sourced from pillow's changelog.
9.3.0 (2022-10-29)
Limit SAMPLESPERPIXEL to avoid runtime DOS #6700 [wiredfool]
Initialize libtiff buffer when saving #6699 [radarhere]
Inline fname2char to fix memory leak #6329 [nulano]
Fix memory leaks related to text features #6330 [nulano]
Use double quotes for version check on old CPython on Windows #6695 [hugovk]
Remove backup implementation of Round for Windows platforms #6693 [cgohlke]
Fixed set_variation_by_name offset #6445 [radarhere]
Fix malloc in _imagingft.c:font_setvaraxes #6690 [cgohlke]
Release Python GIL when converting images using matrix operations #6418 [hmaarrfk]
Added ExifTags enums #6630 [radarhere]
Do not modify previous frame when calculating delta in PNG #6683 [radarhere]
Added support for reading BMP images with RLE4 compression #6674 [npjg, radarhere]
Decode JPEG compressed BLP1 data in original mode #6678 [radarhere]
Added GPS TIFF tag info #6661 [radarhere]
Added conversion between RGB/RGBA/RGBX and LAB #6647 [radarhere]
Do not attempt normalization if mode is already normal #6644 [radarhere]
... (truncated)
d594f4c
Update CHANGES.rst [ci skip]909dc64
9.3.0 version bump1a51ce7
Merge pull request #6699 from hugovk/security-libtiff_buffer2444cdd
Merge pull request #6700 from hugovk/security-samples_per_pixel-sec744f455
Added release notes0846bfa
Add to release notes799a6a0
Fix linting00b25fd
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Bumps py from 1.9.0 to 1.10.0.
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1.10.0 (2020-12-12)
- Fix a regular expression DoS vulnerability in the py.path.svnwc SVN blame functionality (CVE-2020-29651)
- Update vendored apipkg: 1.4 => 1.5
- Update vendored iniconfig: 1.0.0 => 1.1.1
e5ff378
Update CHANGELOG for 1.10.094cf44f
Update vendored libs5e8ded5
testing: comment out an assert which fails on Python 3.9 for nowafdffcc
Rename HOWTORELEASE.rst to RELEASING.rst2de53a6
Merge pull request #266 from nicoddemus/gh-actionsfa1b32e
Merge pull request #264 from hugovk/patch-2887d6b8
Skip test_samefile_symlink on pypy3 on Windowse94e670
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Adapt test4a694b0
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Bumps joblib from 0.16.0 to 1.2.0.
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Release 1.2.0
Fix a security issue where
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Avoid unnecessary warnings when workers and main process delete the temporary memmap folder contents concurrently. joblib/joblib#1263
Fix memory alignment bug for pickles containing numpy arrays. This is especially important when loading the pickle with
mmap_mode != None
as the resultingnumpy.memmap
object would not be able to correct the misalignment without performing a memory copy. This bug would cause invalid computation and segmentation faults with native code that would directly access the underlying data buffer of a numpy array, for instance C/C++/Cython code compiled with older GCC versions or some old OpenBLAS written in platform specific assembly. joblib/joblib#1254Vendor cloudpickle 2.2.0 which adds support for PyPy 3.8+.
Vendor loky 3.3.0 which fixes several bugs including:
robustly forcibly terminating worker processes in case of a crash (joblib/joblib#1269);
avoiding leaking worker processes in case of nested loky parallel calls;
reliability spawn the correct number of reusable workers.
Release 1.1.0
Fix byte order inconsistency issue during deserialization using joblib.load in cross-endian environment: the numpy arrays are now always loaded to use the system byte order, independently of the byte order of the system that serialized the pickle. joblib/joblib#1181
Fix joblib.Memory bug with the
ignore
parameter when the cached function is a decorated function.
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5991350
Release 1.2.03fa2188
MAINT cleanup numpy warnings related to np.matrix in tests (#1340)cea26ff
CI test the future loky-3.3.0 branch (#1338)8aca6f4
MAINT: remove pytest.warns(None) warnings in pytest 7 (#1264)067ed4f
XFAIL test_child_raises_parent_exits_cleanly with multiprocessing (#1339)ac4ebd5
MAINT add back pytest warnings plugin (#1337)a23427d
Test child raises parent exits cleanly more reliable on macos (#1335)ac09691
[MAINT] various test updates (#1334)4a314b1
Vendor loky 3.2.0 (#1333)bdf47e9
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Bumps urllib3 from 1.25.10 to 1.26.5.
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1.26.5
:warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap
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:warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap
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1.26.3
:warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap
Fixed bytes and string comparison issue with headers (Pull #2141)
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1.26.2
:warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap
- Fixed an issue where
wrap_socket
andCERT_REQUIRED
wouldn't be imported properly on Python 2.7.8 and earlier (Pull #2052)1.26.1
:warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap
- Fixed an issue where two
User-Agent
headers would be sent if aUser-Agent
header key is passed asbytes
(Pull #2047)1.26.0
:warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap
Added support for HTTPS proxies contacting HTTPS servers (Pull #1923, Pull #1806)
Deprecated negotiating TLSv1 and TLSv1.1 by default. Users that still wish to use TLS earlier than 1.2 without a deprecation warning should opt-in explicitly by setting
ssl_version=ssl.PROTOCOL_TLSv1_1
(Pull #2002) Starting in urllib3 v2.0: Connections that receive aDeprecationWarning
will failDeprecated
Retry
optionsRetry.DEFAULT_METHOD_WHITELIST
,Retry.DEFAULT_REDIRECT_HEADERS_BLACKLIST
andRetry(method_whitelist=...)
in favor ofRetry.DEFAULT_ALLOWED_METHODS
,Retry.DEFAULT_REMOVE_HEADERS_ON_REDIRECT
, andRetry(allowed_methods=...)
(Pull #2000) Starting in urllib3 v2.0: Deprecated options will be removed
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Sourced from urllib3's changelog.
1.26.5 (2021-05-26)
- Fixed deprecation warnings emitted in Python 3.10.
- Updated vendored
six
library to 1.16.0.- Improved performance of URL parser when splitting the authority component.
1.26.4 (2021-03-15)
- Changed behavior of the default
SSLContext
when connecting to HTTPS proxy during HTTPS requests. The defaultSSLContext
now setscheck_hostname=True
.1.26.3 (2021-01-26)
Fixed bytes and string comparison issue with headers (Pull #2141)
Changed
ProxySchemeUnknown
error message to be more actionable if the user supplies a proxy URL without a scheme. (Pull #2107)1.26.2 (2020-11-12)
- Fixed an issue where
wrap_socket
andCERT_REQUIRED
wouldn't be imported properly on Python 2.7.8 and earlier (Pull #2052)1.26.1 (2020-11-11)
- Fixed an issue where two
User-Agent
headers would be sent if aUser-Agent
header key is passed asbytes
(Pull #2047)1.26.0 (2020-11-10)
NOTE: urllib3 v2.0 will drop support for Python 2.
Read more in the v2.0 Roadmap <https://urllib3.readthedocs.io/en/latest/v2-roadmap.html>
_.Added support for HTTPS proxies contacting HTTPS servers (Pull #1923, Pull #1806)
Deprecated negotiating TLSv1 and TLSv1.1 by default. Users that still wish to use TLS earlier than 1.2 without a deprecation warning
... (truncated)
d161647
Release 1.26.52d4a3fe
Improve performance of sub-authority splitting in URL2698537
Update vendored six to 1.16.007bed79
Fix deprecation warnings for Python 3.10 ssl moduled725a9b
Add Python 3.10 to GitHub Actions339ad34
Use pytest==6.2.4 on Python 3.10+f271c9c
Apply latest Black formatting1884878
[1.26] Properly proxy EOF on the SSLTransport test suitea891304
Release 1.26.48d65ea1
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Machine Learning for Translational Biomedicine group, Toronto
GitHub Repository Homepagemachine-learning imaging-mass-cytometry multiplexed-imaging