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Cell segmentation benchmark

Structure of this repository

  • cellseg_benchmark Function definitions (the package)
  • scripts Scripts for metric calculations and segmentation algorithms, incl. scripts/sbatch_utils for generating per-method sbatch scripts
  • notebooks Jupyter notebooks for development and analysis
  • configs Configuration files (e.g. VPT segmentation configs)
  • archive Symlink to raw MERSCOPE data on DSS
  • data Symlink to processed data on DSS

Development

We are using ruff and the ruff pre-commit hook to check and format the code and docstrings

Installation: Install ruff and pre-commit in your environment and install the pre-commit hooks for ruff defined in .pre-commit-config.yml

pip install ruff
pip install pre-commit
pre-commit install
# (optional: run against all files & fix any errors that are in your current codebase)
pre-commit run --all-files

Basic usage: The ruff config is located in pyproject.toml. See the ruff documentation of rules for all possible rules that we can enable / disable. As we have installed the pre-commit hook, ruff formatting and liniting will run automatically for all changed files whenever you do git commit. If there are errors, you will get a detailled messaged of the offending code and the error. Fix the errors, add the changed file and try to commit again.

You can also manually run the ruff formatter and checker on all files with:

ruff format
ruff check --fix

or

pre-commit run --all-files

If necessary, you can also temporarily disable all pre-commit hooks when committing by using the --no-verify flag with git commit.

About

Spatial Transcriptomics Cell Segmentation Benchmark

Resources

Readme
Activity

Stars

2 stars

Watchers

2 watching

Forks

2 forks
Report repository

Releases

Packages

Used by

Contributors

Languages

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(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
BranchesTags
Repository files navigation
Cell segmentation benchmark
Structure of this repository
  • cellseg_benchmark
Function definitions (the package)
  • scripts
Scripts for metric calculations and segmentation algorithms, incl. scripts/sbatch_utils for generating per-method sbatch scripts
  • notebooks
Jupyter notebooks for development and analysis
  • configs
Configuration files (e.g. VPT segmentation configs)
  • archive
Symlink to raw MERSCOPE data on DSS
  • data
Symlink to processed data on DSS
Development
We are using ruff and the ruff pre-commit hook to check and format the code and docstrings
Installation: Install ruff and pre-commit in your environment and install the pre-commit hooks for ruff defined in .pre-commit-config.yml
pip install ruff
pip install pre-commit
pre-commit install
# (optional: run against all files & fix any errors that are in your current codebase)
pre-commit run --all-files

Basic usage: The ruff config is located in pyproject.toml. See the ruff documentation of rules for all possible rules that we can enable / disable.
As we have installed the pre-commit hook, ruff formatting and liniting will run automatically for all changed files whenever you do git commit. If there are errors, you will get a detailled messaged of the offending code and the error. Fix the errors, add the changed file and try to commit again.
You can also manually run the ruff formatter and checker on all files with:
ruff format
ruff check --fix

or
pre-commit run --all-files

If necessary, you can also temporarily disable all pre-commit hooks when committing by using the --no-verify flag with git commit.
About
Spatial Transcriptomics Cell Segmentation Benchmark
Resources
Readme
Activity
Stars
2 stars
Watchers
2 watching
Forks
2 forks
Report repository
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Used by
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, 'i');
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
Cell segmentation benchmark
Structure of this repository
  • cellseg_benchmark
Function definitions (the package)
  • scripts
Scripts for metric calculations and segmentation algorithms, incl. scripts/sbatch_utils for generating per-method sbatch scripts
  • notebooks
Jupyter notebooks for development and analysis
  • configs
Configuration files (e.g. VPT segmentation configs)
  • archive
Symlink to raw MERSCOPE data on DSS
  • data
Symlink to processed data on DSS
Development
We are using ruff and the ruff pre-commit hook to check and format the code and docstrings
Installation: Install ruff and pre-commit in your environment and install the pre-commit hooks for ruff defined in .pre-commit-config.yml
pip install ruff
pip install pre-commit
pre-commit install
# (optional: run against all files & fix any errors that are in your current codebase)
pre-commit run --all-files

Basic usage: The ruff config is located in pyproject.toml. See the ruff documentation of rules for all possible rules that we can enable / disable.
As we have installed the pre-commit hook, ruff formatting and liniting will run automatically for all changed files whenever you do git commit. If there are errors, you will get a detailled messaged of the offending code and the error. Fix the errors, add the changed file and try to commit again.
You can also manually run the ruff formatter and checker on all files with:
ruff format
ruff check --fix

or
pre-commit run --all-files

If necessary, you can also temporarily disable all pre-commit hooks when committing by using the --no-verify flag with git commit.
About
Spatial Transcriptomics Cell Segmentation Benchmark
Resources
Readme
Activity
Stars
2 stars
Watchers
2 watching
Forks
2 forks
Report repository
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Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Highlight search terms from Google/DuckDuckGo/Bing referrer
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observer.observe(document.body, { childList: true, subtree: true });
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} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
Cell segmentation benchmark
Structure of this repository
  • cellseg_benchmark
Function definitions (the package)
  • scripts
Scripts for metric calculations and segmentation algorithms, incl. scripts/sbatch_utils for generating per-method sbatch scripts
  • notebooks
Jupyter notebooks for development and analysis
  • configs
Configuration files (e.g. VPT segmentation configs)
  • archive
Symlink to raw MERSCOPE data on DSS
  • data
Symlink to processed data on DSS
Development
We are using ruff and the ruff pre-commit hook to check and format the code and docstrings
Installation: Install ruff and pre-commit in your environment and install the pre-commit hooks for ruff defined in .pre-commit-config.yml
pip install ruff
pip install pre-commit
pre-commit install
# (optional: run against all files & fix any errors that are in your current codebase)
pre-commit run --all-files

Basic usage: The ruff config is located in pyproject.toml. See the ruff documentation of rules for all possible rules that we can enable / disable.
As we have installed the pre-commit hook, ruff formatting and liniting will run automatically for all changed files whenever you do git commit. If there are errors, you will get a detailled messaged of the offending code and the error. Fix the errors, add the changed file and try to commit again.
You can also manually run the ruff formatter and checker on all files with:
ruff format
ruff check --fix

or
pre-commit run --all-files

If necessary, you can also temporarily disable all pre-commit hooks when committing by using the --no-verify flag with git commit.
About
Spatial Transcriptomics Cell Segmentation Benchmark
Resources
Readme
Activity
Stars
2 stars
Watchers
2 watching
Forks
2 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
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'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',
'ref', 'ref_src', 'source', 'medium', 'campaign'];
function cleanUrl(url) {
try {
var u = new URL(url, window.location.origin);
var changed = false;
trackingParams.forEach(function(p) {
if (u.searchParams.has(p)) {
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observer.observe(document.body, { childList: true, subtree: true });
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} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
BranchesTags
Repository files navigation
Cell segmentation benchmark
Structure of this repository
  • cellseg_benchmark
Function definitions (the package)
  • scripts
Scripts for metric calculations and segmentation algorithms, incl. scripts/sbatch_utils for generating per-method sbatch scripts
  • notebooks
Jupyter notebooks for development and analysis
  • configs
Configuration files (e.g. VPT segmentation configs)
  • archive
Symlink to raw MERSCOPE data on DSS
  • data
Symlink to processed data on DSS
Development
We are using ruff and the ruff pre-commit hook to check and format the code and docstrings
Installation: Install ruff and pre-commit in your environment and install the pre-commit hooks for ruff defined in .pre-commit-config.yml
pip install ruff
pip install pre-commit
pre-commit install
# (optional: run against all files & fix any errors that are in your current codebase)
pre-commit run --all-files

Basic usage: The ruff config is located in pyproject.toml. See the ruff documentation of rules for all possible rules that we can enable / disable.
As we have installed the pre-commit hook, ruff formatting and liniting will run automatically for all changed files whenever you do git commit. If there are errors, you will get a detailled messaged of the offending code and the error. Fix the errors, add the changed file and try to commit again.
You can also manually run the ruff formatter and checker on all files with:
ruff format
ruff check --fix

or
pre-commit run --all-files

If necessary, you can also temporarily disable all pre-commit hooks when committing by using the --no-verify flag with git commit.
About
Spatial Transcriptomics Cell Segmentation Benchmark
Resources
Readme
Activity
Stars
2 stars
Watchers
2 watching
Forks
2 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
Cell segmentation benchmark
Structure of this repository
  • cellseg_benchmark
Function definitions (the package)
  • scripts
Scripts for metric calculations and segmentation algorithms, incl. scripts/sbatch_utils for generating per-method sbatch scripts
  • notebooks
Jupyter notebooks for development and analysis
  • configs
Configuration files (e.g. VPT segmentation configs)
  • archive
Symlink to raw MERSCOPE data on DSS
  • data
Symlink to processed data on DSS
Development
We are using ruff and the ruff pre-commit hook to check and format the code and docstrings
Installation: Install ruff and pre-commit in your environment and install the pre-commit hooks for ruff defined in .pre-commit-config.yml
pip install ruff
pip install pre-commit
pre-commit install
# (optional: run against all files & fix any errors that are in your current codebase)
pre-commit run --all-files

Basic usage: The ruff config is located in pyproject.toml. See the ruff documentation of rules for all possible rules that we can enable / disable.
As we have installed the pre-commit hook, ruff formatting and liniting will run automatically for all changed files whenever you do git commit. If there are errors, you will get a detailled messaged of the offending code and the error. Fix the errors, add the changed file and try to commit again.
You can also manually run the ruff formatter and checker on all files with:
ruff format
ruff check --fix

or
pre-commit run --all-files

If necessary, you can also temporarily disable all pre-commit hooks when committing by using the --no-verify flag with git commit.
About
Spatial Transcriptomics Cell Segmentation Benchmark
Resources
Readme
Activity
Stars
2 stars
Watchers
2 watching
Forks
2 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Remove or un-stick sticky/fixed headers that block content
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function unstick() {
document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) {
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
Cell segmentation benchmark
Structure of this repository
  • cellseg_benchmark
Function definitions (the package)
  • scripts
Scripts for metric calculations and segmentation algorithms, incl. scripts/sbatch_utils for generating per-method sbatch scripts
  • notebooks
Jupyter notebooks for development and analysis
  • configs
Configuration files (e.g. VPT segmentation configs)
  • archive
Symlink to raw MERSCOPE data on DSS
  • data
Symlink to processed data on DSS
Development
We are using ruff and the ruff pre-commit hook to check and format the code and docstrings
Installation: Install ruff and pre-commit in your environment and install the pre-commit hooks for ruff defined in .pre-commit-config.yml
pip install ruff
pip install pre-commit
pre-commit install
# (optional: run against all files & fix any errors that are in your current codebase)
pre-commit run --all-files

Basic usage: The ruff config is located in pyproject.toml. See the ruff documentation of rules for all possible rules that we can enable / disable.
As we have installed the pre-commit hook, ruff formatting and liniting will run automatically for all changed files whenever you do git commit. If there are errors, you will get a detailled messaged of the offending code and the error. Fix the errors, add the changed file and try to commit again.
You can also manually run the ruff formatter and checker on all files with:
ruff format
ruff check --fix

or
pre-commit run --all-files

If necessary, you can also temporarily disable all pre-commit hooks when committing by using the --no-verify flag with git commit.
About
Spatial Transcriptomics Cell Segmentation Benchmark
Resources
Readme
Activity
Stars
2 stars
Watchers
2 watching
Forks
2 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Universal Dark Mode - works on any site
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var enabled = true;
function applyDarkMode() {
if (!enabled) return;
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if (!style) {
style = document.createElement('style');
style.id = 'universal-dark-mode-style';
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console.log('[Universal Dark Mode] Disabled');
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applyDarkMode();
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var observer = new MutationObserver(function(mutations) {
if (enabled && !document.getElementById('universal-dark-mode-style')) {
applyDarkMode();
}
});
observer.observe(document.head, { childList: true });
console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');
})();
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
BranchesTags
Repository files navigation
Cell segmentation benchmark
Structure of this repository
  • cellseg_benchmark
Function definitions (the package)
  • scripts
Scripts for metric calculations and segmentation algorithms, incl. scripts/sbatch_utils for generating per-method sbatch scripts
  • notebooks
Jupyter notebooks for development and analysis
  • configs
Configuration files (e.g. VPT segmentation configs)
  • archive
Symlink to raw MERSCOPE data on DSS
  • data
Symlink to processed data on DSS
Development
We are using ruff and the ruff pre-commit hook to check and format the code and docstrings
Installation: Install ruff and pre-commit in your environment and install the pre-commit hooks for ruff defined in .pre-commit-config.yml
pip install ruff
pip install pre-commit
pre-commit install
# (optional: run against all files & fix any errors that are in your current codebase)
pre-commit run --all-files

Basic usage: The ruff config is located in pyproject.toml. See the ruff documentation of rules for all possible rules that we can enable / disable.
As we have installed the pre-commit hook, ruff formatting and liniting will run automatically for all changed files whenever you do git commit. If there are errors, you will get a detailled messaged of the offending code and the error. Fix the errors, add the changed file and try to commit again.
You can also manually run the ruff formatter and checker on all files with:
ruff format
ruff check --fix

or
pre-commit run --all-files

If necessary, you can also temporarily disable all pre-commit hooks when committing by using the --no-verify flag with git commit.
About
Spatial Transcriptomics Cell Segmentation Benchmark
Resources
Readme
Activity
Stars
2 stars
Watchers
2 watching
Forks
2 forks
Report repository
Releases
Packages
Used by
Contributors
Languages