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TissueMask

R-CMD-checkpkgdownLicense: MIT

TissueMask fits polygon spatial masks to XY point coordinate data — cell centroids, single-molecule transcript locations, or any spatial point process — and returns an sf geometry object that faithfully captures tissue shape, including internal voids (vessel lumens, necrotic cores) and disconnected fragments.

It is the first component of the TissueSuite family developed at the Raredon Laboratory, Yale School of Medicine.

Installation

# Install from GitHub (requires pak)# install.packages("pak")pak::pkg_install("RaredonLab/TissueMask")

Optional method dependencies:

install.packages(c("concaveman", "MASS", "isoband", "ggplot2"))

Quick start

library(TissueMask)
library(sf)
set.seed(42)
coords<-data.frame(
x= c(rnorm(500, 0, 5), rnorm(500, 20, 5)),
y= c(rnorm(500, 0, 5), rnorm(500, 20, 5))
)
# Fit mask with the recommended raster methodmask<- fit_spatial_mask(coords, method="raster", plot=TRUE)
# Confirm all points are containedpts<-sf::st_as_sf(coords, coords= c("x", "y"), crs=sf::NA_crs_)
stopifnot(all(sf::st_within(pts, sf::st_union(mask), sparse=FALSE)[, 1]))

Methods

methodTopologySpeedKey packages
"raster"(default)Holes + islandsFastsf only
"kde"Holes + islandsModerateMASS, isoband
"concave"No holesFastconcaveman
"convex"No holesInstantsf only

Raster method (recommended)

The raster method:

  1. Bins points onto a regular grid.
  2. Convolves the occupancy grid with a 2-D Gaussian of width raster_sigma (in coordinate units).
  3. Thresholds at raster_threshold x max. Cells above threshold are "inside".
  4. Dissolves all "inside" cells via GEOS union — holes and islands emerge from the geometry automatically, with no ring-winding logic required.
  5. Applies a morphological close to smooth the staircase boundary.

Key tuning parameters:

ParameterEffect
raster_sigma upHoles fill in, islands merge, boundary smooths
raster_sigma downHoles and fine structure preserved
raster_threshold upMask shrinks (requires denser coverage)
raster_threshold downMask grows (accepts sparse regions)

Part of TissueSuite

TissueSuite
+-- TissueMask <- you are here
| fit_spatial_mask() -> sf sfc mask geometry
+-- TissueField (depends on TissueMask)
estimate_concentration_field() -> diffusion-clearance PDE solver

Documentation

Full documentation and rendered vignettes: https://raredonlab.github.io/TissueMask/

  • Getting Started — all four methods with worked examples
  • Holes, Islands, and Parameter Tuning — donut, swiss-cheese, and archipelago topologies; raster_sigma sweep

License

MIT (c) Raredon Laboratory, Yale School of Medicine

About

No description, website, or topics provided.

Resources

Readme
Activity

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0 stars

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0 watching

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1 fork
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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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var __re = new RegExp('^' + "github\\.com" + '

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TissueMask
R-CMD-checkpkgdownLicense: MIT
TissueMask fits polygon spatial masks to XY point coordinate data — cell
centroids, single-molecule transcript locations, or any spatial point process
— and returns an sf geometry object that
faithfully captures tissue shape, including internal voids (vessel lumens,
necrotic cores) and disconnected fragments.
It is the first component of the TissueSuite family developed at the
Raredon Laboratory, Yale School of Medicine.
Installation
# Install from GitHub (requires pak)# install.packages("pak")pak::pkg_install("RaredonLab/TissueMask")
Optional method dependencies:
install.packages(c("concaveman", "MASS", "isoband", "ggplot2"))
Quick start
library(TissueMask)
library(sf)
set.seed(42)
coords<-data.frame(
x= c(rnorm(500, 0, 5), rnorm(500, 20, 5)),
y= c(rnorm(500, 0, 5), rnorm(500, 20, 5))
)
# Fit mask with the recommended raster methodmask<- fit_spatial_mask(coords, method="raster", plot=TRUE)
# Confirm all points are containedpts<-sf::st_as_sf(coords, coords= c("x", "y"), crs=sf::NA_crs_)
stopifnot(all(sf::st_within(pts, sf::st_union(mask), sparse=FALSE)[, 1]))
Methods
methodTopologySpeedKey packages
"raster"(default)Holes + islandsFastsf only
"kde"Holes + islandsModerateMASS, isoband
"concave"No holesFastconcaveman
"convex"No holesInstantsf only
Raster method (recommended)
The raster method:
  1. Bins points onto a regular grid.
  2. Convolves the occupancy grid with a 2-D Gaussian of width raster_sigma
(in coordinate units).
  3. Thresholds at raster_threshold x max. Cells above threshold are "inside".
  4. Dissolves all "inside" cells via GEOS union — holes and islands emerge
from the geometry automatically, with no ring-winding logic required.
  5. Applies a morphological close to smooth the staircase boundary.
Key tuning parameters:
ParameterEffect
raster_sigma upHoles fill in, islands merge, boundary smooths
raster_sigma downHoles and fine structure preserved
raster_threshold upMask shrinks (requires denser coverage)
raster_threshold downMask grows (accepts sparse regions)
Part of TissueSuite
TissueSuite
+-- TissueMask <- you are here
| fit_spatial_mask() -> sf sfc mask geometry
+-- TissueField (depends on TissueMask)
estimate_concentration_field() -> diffusion-clearance PDE solver

Documentation
Full documentation and rendered vignettes:
https://raredonlab.github.io/TissueMask/
  • Getting Started — all four methods with worked examples
  • Holes, Islands, and Parameter Tuning — donut, swiss-cheese, and
archipelago topologies; raster_sigma sweep
License
MIT (c) Raredon Laboratory, Yale School of Medicine
About
No description, website, or topics provided.
Resources
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1 fork
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var __re = new RegExp('^' + ".*" + '

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TissueMask
R-CMD-checkpkgdownLicense: MIT
TissueMask fits polygon spatial masks to XY point coordinate data — cell
centroids, single-molecule transcript locations, or any spatial point process
— and returns an sf geometry object that
faithfully captures tissue shape, including internal voids (vessel lumens,
necrotic cores) and disconnected fragments.
It is the first component of the TissueSuite family developed at the
Raredon Laboratory, Yale School of Medicine.
Installation
# Install from GitHub (requires pak)# install.packages("pak")pak::pkg_install("RaredonLab/TissueMask")
Optional method dependencies:
install.packages(c("concaveman", "MASS", "isoband", "ggplot2"))
Quick start
library(TissueMask)
library(sf)
set.seed(42)
coords<-data.frame(
x= c(rnorm(500, 0, 5), rnorm(500, 20, 5)),
y= c(rnorm(500, 0, 5), rnorm(500, 20, 5))
)
# Fit mask with the recommended raster methodmask<- fit_spatial_mask(coords, method="raster", plot=TRUE)
# Confirm all points are containedpts<-sf::st_as_sf(coords, coords= c("x", "y"), crs=sf::NA_crs_)
stopifnot(all(sf::st_within(pts, sf::st_union(mask), sparse=FALSE)[, 1]))
Methods
methodTopologySpeedKey packages
"raster"(default)Holes + islandsFastsf only
"kde"Holes + islandsModerateMASS, isoband
"concave"No holesFastconcaveman
"convex"No holesInstantsf only
Raster method (recommended)
The raster method:
  1. Bins points onto a regular grid.
  2. Convolves the occupancy grid with a 2-D Gaussian of width raster_sigma
(in coordinate units).
  3. Thresholds at raster_threshold x max. Cells above threshold are "inside".
  4. Dissolves all "inside" cells via GEOS union — holes and islands emerge
from the geometry automatically, with no ring-winding logic required.
  5. Applies a morphological close to smooth the staircase boundary.
Key tuning parameters:
ParameterEffect
raster_sigma upHoles fill in, islands merge, boundary smooths
raster_sigma downHoles and fine structure preserved
raster_threshold upMask shrinks (requires denser coverage)
raster_threshold downMask grows (accepts sparse regions)
Part of TissueSuite
TissueSuite
+-- TissueMask <- you are here
| fit_spatial_mask() -> sf sfc mask geometry
+-- TissueField (depends on TissueMask)
estimate_concentration_field() -> diffusion-clearance PDE solver

Documentation
Full documentation and rendered vignettes:
https://raredonlab.github.io/TissueMask/
  • Getting Started — all four methods with worked examples
  • Holes, Islands, and Parameter Tuning — donut, swiss-cheese, and
archipelago topologies; raster_sigma sweep
License
MIT (c) Raredon Laboratory, Yale School of Medicine
About
No description, website, or topics provided.
Resources
Readme
Activity
Stars
0 stars
Watchers
0 watching
Forks
1 fork
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if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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TissueMask
R-CMD-checkpkgdownLicense: MIT
TissueMask fits polygon spatial masks to XY point coordinate data — cell
centroids, single-molecule transcript locations, or any spatial point process
— and returns an sf geometry object that
faithfully captures tissue shape, including internal voids (vessel lumens,
necrotic cores) and disconnected fragments.
It is the first component of the TissueSuite family developed at the
Raredon Laboratory, Yale School of Medicine.
Installation
# Install from GitHub (requires pak)# install.packages("pak")pak::pkg_install("RaredonLab/TissueMask")
Optional method dependencies:
install.packages(c("concaveman", "MASS", "isoband", "ggplot2"))
Quick start
library(TissueMask)
library(sf)
set.seed(42)
coords<-data.frame(
x= c(rnorm(500, 0, 5), rnorm(500, 20, 5)),
y= c(rnorm(500, 0, 5), rnorm(500, 20, 5))
)
# Fit mask with the recommended raster methodmask<- fit_spatial_mask(coords, method="raster", plot=TRUE)
# Confirm all points are containedpts<-sf::st_as_sf(coords, coords= c("x", "y"), crs=sf::NA_crs_)
stopifnot(all(sf::st_within(pts, sf::st_union(mask), sparse=FALSE)[, 1]))
Methods
methodTopologySpeedKey packages
"raster"(default)Holes + islandsFastsf only
"kde"Holes + islandsModerateMASS, isoband
"concave"No holesFastconcaveman
"convex"No holesInstantsf only
Raster method (recommended)
The raster method:
  1. Bins points onto a regular grid.
  2. Convolves the occupancy grid with a 2-D Gaussian of width raster_sigma
(in coordinate units).
  3. Thresholds at raster_threshold x max. Cells above threshold are "inside".
  4. Dissolves all "inside" cells via GEOS union — holes and islands emerge
from the geometry automatically, with no ring-winding logic required.
  5. Applies a morphological close to smooth the staircase boundary.
Key tuning parameters:
ParameterEffect
raster_sigma upHoles fill in, islands merge, boundary smooths
raster_sigma downHoles and fine structure preserved
raster_threshold upMask shrinks (requires denser coverage)
raster_threshold downMask grows (accepts sparse regions)
Part of TissueSuite
TissueSuite
+-- TissueMask <- you are here
| fit_spatial_mask() -> sf sfc mask geometry
+-- TissueField (depends on TissueMask)
estimate_concentration_field() -> diffusion-clearance PDE solver

Documentation
Full documentation and rendered vignettes:
https://raredonlab.github.io/TissueMask/
  • Getting Started — all four methods with worked examples
  • Holes, Islands, and Parameter Tuning — donut, swiss-cheese, and
archipelago topologies; raster_sigma sweep
License
MIT (c) Raredon Laboratory, Yale School of Medicine
About
No description, website, or topics provided.
Resources
Readme
Activity
Stars
0 stars
Watchers
0 watching
Forks
1 fork
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
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try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

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TissueMask
R-CMD-checkpkgdownLicense: MIT
TissueMask fits polygon spatial masks to XY point coordinate data — cell
centroids, single-molecule transcript locations, or any spatial point process
— and returns an sf geometry object that
faithfully captures tissue shape, including internal voids (vessel lumens,
necrotic cores) and disconnected fragments.
It is the first component of the TissueSuite family developed at the
Raredon Laboratory, Yale School of Medicine.
Installation
# Install from GitHub (requires pak)# install.packages("pak")pak::pkg_install("RaredonLab/TissueMask")
Optional method dependencies:
install.packages(c("concaveman", "MASS", "isoband", "ggplot2"))
Quick start
library(TissueMask)
library(sf)
set.seed(42)
coords<-data.frame(
x= c(rnorm(500, 0, 5), rnorm(500, 20, 5)),
y= c(rnorm(500, 0, 5), rnorm(500, 20, 5))
)
# Fit mask with the recommended raster methodmask<- fit_spatial_mask(coords, method="raster", plot=TRUE)
# Confirm all points are containedpts<-sf::st_as_sf(coords, coords= c("x", "y"), crs=sf::NA_crs_)
stopifnot(all(sf::st_within(pts, sf::st_union(mask), sparse=FALSE)[, 1]))
Methods
methodTopologySpeedKey packages
"raster"(default)Holes + islandsFastsf only
"kde"Holes + islandsModerateMASS, isoband
"concave"No holesFastconcaveman
"convex"No holesInstantsf only
Raster method (recommended)
The raster method:
  1. Bins points onto a regular grid.
  2. Convolves the occupancy grid with a 2-D Gaussian of width raster_sigma
(in coordinate units).
  3. Thresholds at raster_threshold x max. Cells above threshold are "inside".
  4. Dissolves all "inside" cells via GEOS union — holes and islands emerge
from the geometry automatically, with no ring-winding logic required.
  5. Applies a morphological close to smooth the staircase boundary.
Key tuning parameters:
ParameterEffect
raster_sigma upHoles fill in, islands merge, boundary smooths
raster_sigma downHoles and fine structure preserved
raster_threshold upMask shrinks (requires denser coverage)
raster_threshold downMask grows (accepts sparse regions)
Part of TissueSuite
TissueSuite
+-- TissueMask <- you are here
| fit_spatial_mask() -> sf sfc mask geometry
+-- TissueField (depends on TissueMask)
estimate_concentration_field() -> diffusion-clearance PDE solver

Documentation
Full documentation and rendered vignettes:
https://raredonlab.github.io/TissueMask/
  • Getting Started — all four methods with worked examples
  • Holes, Islands, and Parameter Tuning — donut, swiss-cheese, and
archipelago topologies; raster_sigma sweep
License
MIT (c) Raredon Laboratory, Yale School of Medicine
About
No description, website, or topics provided.
Resources
Readme
Activity
Stars
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Watchers
0 watching
Forks
1 fork
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
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var __re = new RegExp('^' + ".*" + '

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TissueMask
R-CMD-checkpkgdownLicense: MIT
TissueMask fits polygon spatial masks to XY point coordinate data — cell
centroids, single-molecule transcript locations, or any spatial point process
— and returns an sf geometry object that
faithfully captures tissue shape, including internal voids (vessel lumens,
necrotic cores) and disconnected fragments.
It is the first component of the TissueSuite family developed at the
Raredon Laboratory, Yale School of Medicine.
Installation
# Install from GitHub (requires pak)# install.packages("pak")pak::pkg_install("RaredonLab/TissueMask")
Optional method dependencies:
install.packages(c("concaveman", "MASS", "isoband", "ggplot2"))
Quick start
library(TissueMask)
library(sf)
set.seed(42)
coords<-data.frame(
x= c(rnorm(500, 0, 5), rnorm(500, 20, 5)),
y= c(rnorm(500, 0, 5), rnorm(500, 20, 5))
)
# Fit mask with the recommended raster methodmask<- fit_spatial_mask(coords, method="raster", plot=TRUE)
# Confirm all points are containedpts<-sf::st_as_sf(coords, coords= c("x", "y"), crs=sf::NA_crs_)
stopifnot(all(sf::st_within(pts, sf::st_union(mask), sparse=FALSE)[, 1]))
Methods
methodTopologySpeedKey packages
"raster"(default)Holes + islandsFastsf only
"kde"Holes + islandsModerateMASS, isoband
"concave"No holesFastconcaveman
"convex"No holesInstantsf only
Raster method (recommended)
The raster method:
  1. Bins points onto a regular grid.
  2. Convolves the occupancy grid with a 2-D Gaussian of width raster_sigma
(in coordinate units).
  3. Thresholds at raster_threshold x max. Cells above threshold are "inside".
  4. Dissolves all "inside" cells via GEOS union — holes and islands emerge
from the geometry automatically, with no ring-winding logic required.
  5. Applies a morphological close to smooth the staircase boundary.
Key tuning parameters:
ParameterEffect
raster_sigma upHoles fill in, islands merge, boundary smooths
raster_sigma downHoles and fine structure preserved
raster_threshold upMask shrinks (requires denser coverage)
raster_threshold downMask grows (accepts sparse regions)
Part of TissueSuite
TissueSuite
+-- TissueMask <- you are here
| fit_spatial_mask() -> sf sfc mask geometry
+-- TissueField (depends on TissueMask)
estimate_concentration_field() -> diffusion-clearance PDE solver

Documentation
Full documentation and rendered vignettes:
https://raredonlab.github.io/TissueMask/
  • Getting Started — all four methods with worked examples
  • Holes, Islands, and Parameter Tuning — donut, swiss-cheese, and
archipelago topologies; raster_sigma sweep
License
MIT (c) Raredon Laboratory, Yale School of Medicine
About
No description, website, or topics provided.
Resources
Readme
Activity
Stars
0 stars
Watchers
0 watching
Forks
1 fork
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Releases
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Contributors
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injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
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} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
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TissueMask
R-CMD-checkpkgdownLicense: MIT
TissueMask fits polygon spatial masks to XY point coordinate data — cell
centroids, single-molecule transcript locations, or any spatial point process
— and returns an sf geometry object that
faithfully captures tissue shape, including internal voids (vessel lumens,
necrotic cores) and disconnected fragments.
It is the first component of the TissueSuite family developed at the
Raredon Laboratory, Yale School of Medicine.
Installation
# Install from GitHub (requires pak)# install.packages("pak")pak::pkg_install("RaredonLab/TissueMask")
Optional method dependencies:
install.packages(c("concaveman", "MASS", "isoband", "ggplot2"))
Quick start
library(TissueMask)
library(sf)
set.seed(42)
coords<-data.frame(
x= c(rnorm(500, 0, 5), rnorm(500, 20, 5)),
y= c(rnorm(500, 0, 5), rnorm(500, 20, 5))
)
# Fit mask with the recommended raster methodmask<- fit_spatial_mask(coords, method="raster", plot=TRUE)
# Confirm all points are containedpts<-sf::st_as_sf(coords, coords= c("x", "y"), crs=sf::NA_crs_)
stopifnot(all(sf::st_within(pts, sf::st_union(mask), sparse=FALSE)[, 1]))
Methods
methodTopologySpeedKey packages
"raster"(default)Holes + islandsFastsf only
"kde"Holes + islandsModerateMASS, isoband
"concave"No holesFastconcaveman
"convex"No holesInstantsf only
Raster method (recommended)
The raster method:
  1. Bins points onto a regular grid.
  2. Convolves the occupancy grid with a 2-D Gaussian of width raster_sigma
(in coordinate units).
  3. Thresholds at raster_threshold x max. Cells above threshold are "inside".
  4. Dissolves all "inside" cells via GEOS union — holes and islands emerge
from the geometry automatically, with no ring-winding logic required.
  5. Applies a morphological close to smooth the staircase boundary.
Key tuning parameters:
ParameterEffect
raster_sigma upHoles fill in, islands merge, boundary smooths
raster_sigma downHoles and fine structure preserved
raster_threshold upMask shrinks (requires denser coverage)
raster_threshold downMask grows (accepts sparse regions)
Part of TissueSuite
TissueSuite
+-- TissueMask <- you are here
| fit_spatial_mask() -> sf sfc mask geometry
+-- TissueField (depends on TissueMask)
estimate_concentration_field() -> diffusion-clearance PDE solver

Documentation
Full documentation and rendered vignettes:
https://raredonlab.github.io/TissueMask/
  • Getting Started — all four methods with worked examples
  • Holes, Islands, and Parameter Tuning — donut, swiss-cheese, and
archipelago topologies; raster_sigma sweep
License
MIT (c) Raredon Laboratory, Yale School of Medicine
About
No description, website, or topics provided.
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Readme
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TissueMask
R-CMD-checkpkgdownLicense: MIT
TissueMask fits polygon spatial masks to XY point coordinate data — cell
centroids, single-molecule transcript locations, or any spatial point process
— and returns an sf geometry object that
faithfully captures tissue shape, including internal voids (vessel lumens,
necrotic cores) and disconnected fragments.
It is the first component of the TissueSuite family developed at the
Raredon Laboratory, Yale School of Medicine.
Installation
# Install from GitHub (requires pak)# install.packages("pak")pak::pkg_install("RaredonLab/TissueMask")
Optional method dependencies:
install.packages(c("concaveman", "MASS", "isoband", "ggplot2"))
Quick start
library(TissueMask)
library(sf)
set.seed(42)
coords<-data.frame(
x= c(rnorm(500, 0, 5), rnorm(500, 20, 5)),
y= c(rnorm(500, 0, 5), rnorm(500, 20, 5))
)
# Fit mask with the recommended raster methodmask<- fit_spatial_mask(coords, method="raster", plot=TRUE)
# Confirm all points are containedpts<-sf::st_as_sf(coords, coords= c("x", "y"), crs=sf::NA_crs_)
stopifnot(all(sf::st_within(pts, sf::st_union(mask), sparse=FALSE)[, 1]))
Methods
methodTopologySpeedKey packages
"raster"(default)Holes + islandsFastsf only
"kde"Holes + islandsModerateMASS, isoband
"concave"No holesFastconcaveman
"convex"No holesInstantsf only
Raster method (recommended)
The raster method:
  1. Bins points onto a regular grid.
  2. Convolves the occupancy grid with a 2-D Gaussian of width raster_sigma
(in coordinate units).
  3. Thresholds at raster_threshold x max. Cells above threshold are "inside".
  4. Dissolves all "inside" cells via GEOS union — holes and islands emerge
from the geometry automatically, with no ring-winding logic required.
  5. Applies a morphological close to smooth the staircase boundary.
Key tuning parameters:
ParameterEffect
raster_sigma upHoles fill in, islands merge, boundary smooths
raster_sigma downHoles and fine structure preserved
raster_threshold upMask shrinks (requires denser coverage)
raster_threshold downMask grows (accepts sparse regions)
Part of TissueSuite
TissueSuite
+-- TissueMask <- you are here
| fit_spatial_mask() -> sf sfc mask geometry
+-- TissueField (depends on TissueMask)
estimate_concentration_field() -> diffusion-clearance PDE solver

Documentation
Full documentation and rendered vignettes:
https://raredonlab.github.io/TissueMask/
  • Getting Started — all four methods with worked examples
  • Holes, Islands, and Parameter Tuning — donut, swiss-cheese, and
archipelago topologies; raster_sigma sweep
License
MIT (c) Raredon Laboratory, Yale School of Medicine
About
No description, website, or topics provided.
Resources
Readme
Activity
Stars
0 stars
Watchers
0 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors
Languages