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v0.6.3 #83

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6000966
start a new dev version
Henley13 Apr 25, 2022
e102ac2
update requirement pandas
Henley13 May 10, 2022
c422251
fix #77 by updating readme and doc for python version >3.6
Henley13 Sep 5, 2022
9da2041
update documentation to fix big-fish-examples#11
Henley13 Sep 5, 2022
eee0500
fix tensorflow import with python 3.9 by unpinning dependencies
Henley13 Sep 5, 2022
cb8b646
update citation
Henley13 Sep 5, 2022
ef86b65
close #76
Henley13 Jul 3, 2023
04fc249
Adapt cell extraction techniques for 3D masks
Henley13 Jul 4, 2023
6c29443
adapt bigfish.multistack.postprocess to 3D masks
Henley13 Jul 5, 2023
835c596
adapt bigfish.multistack.postprocess to 3D masks
Henley13 Jul 5, 2023
eb84465
adapt bigfish.multistack.postprocess to 3D masks
Henley13 Jul 5, 2023
b7655f6
adapt bigfish.multistack.postprocess to 3D masks
Henley13 Jul 5, 2023
c398ad3
add python 3.10 to be tested
Henley13 Jul 5, 2023
9e119b0
fix #82 import error with newer version of scikit-image
Henley13 Jul 6, 2023
cd0e70e
fix bug saving png, jpg and jpeg
Henley13 Jul 6, 2023
4fcc688
update readme (mail and url)
Henley13 Jul 6, 2023
1862ab5
add citation file
Henley13 Jul 6, 2023
15266f1
update citation
Henley13 Jul 6, 2023
77edd89
update readme
Henley13 Jul 6, 2023
3aa8397
update readme
Henley13 Jul 6, 2023
99cbc24
define workflow with github action to run tests
Henley13 Jul 6, 2023
ebf4c1a
fix os and python version compatibility in workflows
Henley13 Jul 6, 2023
16073b3
fix os and python version compatibility in workflows
Henley13 Jul 6, 2023
cdec0bf
fix os and python version compatibility in workflows
Henley13 Jul 6, 2023
ee8d4b6
remove travis file
Henley13 Jul 6, 2023
6d4d9bb
update CI badge
Henley13 Jul 7, 2023
0f830f2
reformart code with black
Henley13 Jul 7, 2023
3d8a992
Avoiding ruining git blame
Henley13 Jul 7, 2023
0865b86
config ruff as python linter
Henley13 Jul 7, 2023
ac9958e
config ruff as python linter
Henley13 Jul 7, 2023
bc75274
fix linter warnings
Henley13 Jul 7, 2023
88b8642
fix spelling mistakes
Henley13 Jul 7, 2023
2e6ba3d
add ruff badge
Henley13 Jul 7, 2023
7d1a7f0
misc
Henley13 Jul 7, 2023
37bd00f
implement a github workflow to build/upload package to Pypi
Henley13 Jul 10, 2023
bbdf52e
implement a github workflow to build/upload package to Pypi
Henley13 Jul 10, 2023
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add ruff badge
Henley13 committed Jul 7, 2023
commit 2e6ba3d4482327f5f1edca5be5dbaf14781c5562
1 change: 1 addition & 0 deletions README.md
Original file line number Diff line number Diff line change
@@ -7,6 +7,7 @@
[![License](https://img.shields.io/badge/license-BSD%203--Clause-green)](https://github.com/fish-quant/big-fish/blob/master/LICENSE)
[![Python version](https://img.shields.io/pypi/pyversions/big-fish.svg)](https://pypi.python.org/pypi/big-fish/)
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)

**Big-FISH** is a python package for the analysis of smFISH images. It includes various methods to **analyze microscopy images**, such **spot detection** and **segmentation of cells and nuclei**. The package allows the user represent the extract properties of a cell as coordinates (see figure below). The ultimate goal is to simplify **large scale statistical analysis** and quantification.