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Overview

Collaborative Segmentation Software

A browser-based online annotation tool for 3D medical image volumes that allow annotations to be shared between users. The sharing feature allows images to be viewed across multiple users concurrently, and can sync viewing perspectives and drawings. For a shared viewing experience, changes made to a volume/image are updated automatically when a drawing is finished or a slice is changed.

The software utilizes Pusher, which eliminates the need for a server to handle real-time functionality.

Website

Documentation

Technologies

Features

The software contains 3 types of synchronization features for easy collaboration:

  • Annotation Sync



  • Perspective View Sync



  • Slice View Sync



  • Simple UI



Loading Medical Volumes

Settings & Controls

FunctionsDescription
Select ColorChanges the color of the pen used to draw annotations
Toggle DrawingEnables and disables the use of the pen
Toggle ErasingEnables and disables the use of the eraser
Change ViewChanges the canvas to display different perspectives of the 3D medical image
UndoRemoves the latest annotation created
Save .nvdSaves the medical image with annotations, can be uploaded to re-annotate
Save .niiSaves the annotations only
Save .pngSaves the current image slice with annotations
Opacity SliderChanges opacity of the annotations: 0 - Clear, 1 - Opaque
Slice CycleChanges the canvas to display different slices of the 3D medical image
ZoomMove closer or further from the canvas
MeasureMeasures length from the starting to ending point with units in millimeters
Sync ViewEnables and disables both annotation and image view sync

Supported Images

FormatsFile Type
VoxelNIfTI, NRRD, MRtrix MIF, AFNI HEAD/BRIK, MGH/MGZ, ITK MHD, ECAT7
MeshGIfTI, ASC, BrainSuite DFS, PLY, BrainNet NV, BrainVoyager SRF, FreeSurfer, MZ3, OFF, Wavefront OBJ, STL, Legacy VTK, X3D
Mesh OverlayGIfTI, CIfTI-2, MZ3, SMP, STC, FreeSurfer (CURV/ANNOT)
TractographyTCK, TRK, TRX, VTK, AFNI .niml.tract
DICOMDICOM, DICOM Manifests



About

A project from CS 410 (Intro to Software Engineering) for Massachusetts General Hospital

Resources

Readme
MIT license
Activity

Stars

2 stars

Watchers

2 watching

Forks

1 fork
Report repository

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Used by

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Languages

, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
BranchesTags
Repository files navigation
Overview
Collaborative Segmentation Software
A browser-based online annotation tool for 3D medical image volumes that allow annotations to be shared between users. The sharing feature allows images to be viewed across multiple users concurrently, and can sync viewing perspectives and drawings. For a shared viewing experience, changes made to a volume/image are updated automatically when a drawing is finished or a slice is changed.
The software utilizes Pusher, which eliminates the need for a server to handle real-time functionality.
Website
Documentation
Technologies
Features
The software contains 3 types of synchronization features for easy collaboration:
  • Annotation Sync



  • Perspective View Sync



  • Slice View Sync



  • Simple UI



Loading Medical Volumes
Settings & Controls
FunctionsDescription
Select ColorChanges the color of the pen used to draw annotations
Toggle DrawingEnables and disables the use of the pen
Toggle ErasingEnables and disables the use of the eraser
Change ViewChanges the canvas to display different perspectives of the 3D medical image
UndoRemoves the latest annotation created
Save .nvdSaves the medical image with annotations, can be uploaded to re-annotate
Save .niiSaves the annotations only
Save .pngSaves the current image slice with annotations
Opacity SliderChanges opacity of the annotations: 0 - Clear, 1 - Opaque
Slice CycleChanges the canvas to display different slices of the 3D medical image
ZoomMove closer or further from the canvas
MeasureMeasures length from the starting to ending point with units in millimeters
Sync ViewEnables and disables both annotation and image view sync
Supported Images
FormatsFile Type
VoxelNIfTI, NRRD, MRtrix MIF, AFNI HEAD/BRIK, MGH/MGZ, ITK MHD, ECAT7
MeshGIfTI, ASC, BrainSuite DFS, PLY, BrainNet NV, BrainVoyager SRF, FreeSurfer, MZ3, OFF, Wavefront OBJ, STL, Legacy VTK, X3D
Mesh OverlayGIfTI, CIfTI-2, MZ3, SMP, STC, FreeSurfer (CURV/ANNOT)
TractographyTCK, TRK, TRX, VTK, AFNI .niml.tract
DICOMDICOM, DICOM Manifests


About
A project from CS 410 (Intro to Software Engineering) for Massachusetts General Hospital
Resources
Readme
MIT license
Activity
Stars
2 stars
Watchers
2 watching
Forks
1 fork
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
Overview
Collaborative Segmentation Software
A browser-based online annotation tool for 3D medical image volumes that allow annotations to be shared between users. The sharing feature allows images to be viewed across multiple users concurrently, and can sync viewing perspectives and drawings. For a shared viewing experience, changes made to a volume/image are updated automatically when a drawing is finished or a slice is changed.
The software utilizes Pusher, which eliminates the need for a server to handle real-time functionality.
Website
Documentation
Technologies
Features
The software contains 3 types of synchronization features for easy collaboration:
  • Annotation Sync



  • Perspective View Sync



  • Slice View Sync



  • Simple UI



Loading Medical Volumes
Settings & Controls
FunctionsDescription
Select ColorChanges the color of the pen used to draw annotations
Toggle DrawingEnables and disables the use of the pen
Toggle ErasingEnables and disables the use of the eraser
Change ViewChanges the canvas to display different perspectives of the 3D medical image
UndoRemoves the latest annotation created
Save .nvdSaves the medical image with annotations, can be uploaded to re-annotate
Save .niiSaves the annotations only
Save .pngSaves the current image slice with annotations
Opacity SliderChanges opacity of the annotations: 0 - Clear, 1 - Opaque
Slice CycleChanges the canvas to display different slices of the 3D medical image
ZoomMove closer or further from the canvas
MeasureMeasures length from the starting to ending point with units in millimeters
Sync ViewEnables and disables both annotation and image view sync
Supported Images
FormatsFile Type
VoxelNIfTI, NRRD, MRtrix MIF, AFNI HEAD/BRIK, MGH/MGZ, ITK MHD, ECAT7
MeshGIfTI, ASC, BrainSuite DFS, PLY, BrainNet NV, BrainVoyager SRF, FreeSurfer, MZ3, OFF, Wavefront OBJ, STL, Legacy VTK, X3D
Mesh OverlayGIfTI, CIfTI-2, MZ3, SMP, STC, FreeSurfer (CURV/ANNOT)
TractographyTCK, TRK, TRX, VTK, AFNI .niml.tract
DICOMDICOM, DICOM Manifests


About
A project from CS 410 (Intro to Software Engineering) for Massachusetts General Hospital
Resources
Readme
MIT license
Activity
Stars
2 stars
Watchers
2 watching
Forks
1 fork
Report repository
Releases
Packages
Used by
Contributors
Languages

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

Skip to content
BranchesTags
Repository files navigation
Overview
Collaborative Segmentation Software
A browser-based online annotation tool for 3D medical image volumes that allow annotations to be shared between users. The sharing feature allows images to be viewed across multiple users concurrently, and can sync viewing perspectives and drawings. For a shared viewing experience, changes made to a volume/image are updated automatically when a drawing is finished or a slice is changed.
The software utilizes Pusher, which eliminates the need for a server to handle real-time functionality.
Website
Documentation
Technologies
Features
The software contains 3 types of synchronization features for easy collaboration:
  • Annotation Sync



  • Perspective View Sync



  • Slice View Sync



  • Simple UI



Loading Medical Volumes
Settings & Controls
FunctionsDescription
Select ColorChanges the color of the pen used to draw annotations
Toggle DrawingEnables and disables the use of the pen
Toggle ErasingEnables and disables the use of the eraser
Change ViewChanges the canvas to display different perspectives of the 3D medical image
UndoRemoves the latest annotation created
Save .nvdSaves the medical image with annotations, can be uploaded to re-annotate
Save .niiSaves the annotations only
Save .pngSaves the current image slice with annotations
Opacity SliderChanges opacity of the annotations: 0 - Clear, 1 - Opaque
Slice CycleChanges the canvas to display different slices of the 3D medical image
ZoomMove closer or further from the canvas
MeasureMeasures length from the starting to ending point with units in millimeters
Sync ViewEnables and disables both annotation and image view sync
Supported Images
FormatsFile Type
VoxelNIfTI, NRRD, MRtrix MIF, AFNI HEAD/BRIK, MGH/MGZ, ITK MHD, ECAT7
MeshGIfTI, ASC, BrainSuite DFS, PLY, BrainNet NV, BrainVoyager SRF, FreeSurfer, MZ3, OFF, Wavefront OBJ, STL, Legacy VTK, X3D
Mesh OverlayGIfTI, CIfTI-2, MZ3, SMP, STC, FreeSurfer (CURV/ANNOT)
TractographyTCK, TRK, TRX, VTK, AFNI .niml.tract
DICOMDICOM, DICOM Manifests


About
A project from CS 410 (Intro to Software Engineering) for Massachusetts General Hospital
Resources
Readme
MIT license
Activity
Stars
2 stars
Watchers
2 watching
Forks
1 fork
Report repository
Releases
Packages
Used by
Contributors
Languages

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

Skip to content
BranchesTags
Repository files navigation
Overview
Collaborative Segmentation Software
A browser-based online annotation tool for 3D medical image volumes that allow annotations to be shared between users. The sharing feature allows images to be viewed across multiple users concurrently, and can sync viewing perspectives and drawings. For a shared viewing experience, changes made to a volume/image are updated automatically when a drawing is finished or a slice is changed.
The software utilizes Pusher, which eliminates the need for a server to handle real-time functionality.
Website
Documentation
Technologies
Features
The software contains 3 types of synchronization features for easy collaboration:
  • Annotation Sync



  • Perspective View Sync



  • Slice View Sync



  • Simple UI



Loading Medical Volumes
Settings & Controls
FunctionsDescription
Select ColorChanges the color of the pen used to draw annotations
Toggle DrawingEnables and disables the use of the pen
Toggle ErasingEnables and disables the use of the eraser
Change ViewChanges the canvas to display different perspectives of the 3D medical image
UndoRemoves the latest annotation created
Save .nvdSaves the medical image with annotations, can be uploaded to re-annotate
Save .niiSaves the annotations only
Save .pngSaves the current image slice with annotations
Opacity SliderChanges opacity of the annotations: 0 - Clear, 1 - Opaque
Slice CycleChanges the canvas to display different slices of the 3D medical image
ZoomMove closer or further from the canvas
MeasureMeasures length from the starting to ending point with units in millimeters
Sync ViewEnables and disables both annotation and image view sync
Supported Images
FormatsFile Type
VoxelNIfTI, NRRD, MRtrix MIF, AFNI HEAD/BRIK, MGH/MGZ, ITK MHD, ECAT7
MeshGIfTI, ASC, BrainSuite DFS, PLY, BrainNet NV, BrainVoyager SRF, FreeSurfer, MZ3, OFF, Wavefront OBJ, STL, Legacy VTK, X3D
Mesh OverlayGIfTI, CIfTI-2, MZ3, SMP, STC, FreeSurfer (CURV/ANNOT)
TractographyTCK, TRK, TRX, VTK, AFNI .niml.tract
DICOMDICOM, DICOM Manifests


About
A project from CS 410 (Intro to Software Engineering) for Massachusetts General Hospital
Resources
Readme
MIT license
Activity
Stars
2 stars
Watchers
2 watching
Forks
1 fork
Report repository
Releases
Packages
Used by
Contributors
Languages

, '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); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
Overview
Collaborative Segmentation Software
A browser-based online annotation tool for 3D medical image volumes that allow annotations to be shared between users. The sharing feature allows images to be viewed across multiple users concurrently, and can sync viewing perspectives and drawings. For a shared viewing experience, changes made to a volume/image are updated automatically when a drawing is finished or a slice is changed.
The software utilizes Pusher, which eliminates the need for a server to handle real-time functionality.
Website
Documentation
Technologies
Features
The software contains 3 types of synchronization features for easy collaboration:
  • Annotation Sync



  • Perspective View Sync



  • Slice View Sync



  • Simple UI



Loading Medical Volumes
Settings & Controls
FunctionsDescription
Select ColorChanges the color of the pen used to draw annotations
Toggle DrawingEnables and disables the use of the pen
Toggle ErasingEnables and disables the use of the eraser
Change ViewChanges the canvas to display different perspectives of the 3D medical image
UndoRemoves the latest annotation created
Save .nvdSaves the medical image with annotations, can be uploaded to re-annotate
Save .niiSaves the annotations only
Save .pngSaves the current image slice with annotations
Opacity SliderChanges opacity of the annotations: 0 - Clear, 1 - Opaque
Slice CycleChanges the canvas to display different slices of the 3D medical image
ZoomMove closer or further from the canvas
MeasureMeasures length from the starting to ending point with units in millimeters
Sync ViewEnables and disables both annotation and image view sync
Supported Images
FormatsFile Type
VoxelNIfTI, NRRD, MRtrix MIF, AFNI HEAD/BRIK, MGH/MGZ, ITK MHD, ECAT7
MeshGIfTI, ASC, BrainSuite DFS, PLY, BrainNet NV, BrainVoyager SRF, FreeSurfer, MZ3, OFF, Wavefront OBJ, STL, Legacy VTK, X3D
Mesh OverlayGIfTI, CIfTI-2, MZ3, SMP, STC, FreeSurfer (CURV/ANNOT)
TractographyTCK, TRK, TRX, VTK, AFNI .niml.tract
DICOMDICOM, DICOM Manifests


About
A project from CS 410 (Intro to Software Engineering) for Massachusetts General Hospital
Resources
Readme
MIT license
Activity
Stars
2 stars
Watchers
2 watching
Forks
1 fork
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
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");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
Overview
Collaborative Segmentation Software
A browser-based online annotation tool for 3D medical image volumes that allow annotations to be shared between users. The sharing feature allows images to be viewed across multiple users concurrently, and can sync viewing perspectives and drawings. For a shared viewing experience, changes made to a volume/image are updated automatically when a drawing is finished or a slice is changed.
The software utilizes Pusher, which eliminates the need for a server to handle real-time functionality.
Website
Documentation
Technologies
Features
The software contains 3 types of synchronization features for easy collaboration:
  • Annotation Sync



  • Perspective View Sync



  • Slice View Sync



  • Simple UI



Loading Medical Volumes
Settings & Controls
FunctionsDescription
Select ColorChanges the color of the pen used to draw annotations
Toggle DrawingEnables and disables the use of the pen
Toggle ErasingEnables and disables the use of the eraser
Change ViewChanges the canvas to display different perspectives of the 3D medical image
UndoRemoves the latest annotation created
Save .nvdSaves the medical image with annotations, can be uploaded to re-annotate
Save .niiSaves the annotations only
Save .pngSaves the current image slice with annotations
Opacity SliderChanges opacity of the annotations: 0 - Clear, 1 - Opaque
Slice CycleChanges the canvas to display different slices of the 3D medical image
ZoomMove closer or further from the canvas
MeasureMeasures length from the starting to ending point with units in millimeters
Sync ViewEnables and disables both annotation and image view sync
Supported Images
FormatsFile Type
VoxelNIfTI, NRRD, MRtrix MIF, AFNI HEAD/BRIK, MGH/MGZ, ITK MHD, ECAT7
MeshGIfTI, ASC, BrainSuite DFS, PLY, BrainNet NV, BrainVoyager SRF, FreeSurfer, MZ3, OFF, Wavefront OBJ, STL, Legacy VTK, X3D
Mesh OverlayGIfTI, CIfTI-2, MZ3, SMP, STC, FreeSurfer (CURV/ANNOT)
TractographyTCK, TRK, TRX, VTK, AFNI .niml.tract
DICOMDICOM, DICOM Manifests


About
A project from CS 410 (Intro to Software Engineering) for Massachusetts General Hospital
Resources
Readme
MIT license
Activity
Stars
2 stars
Watchers
2 watching
Forks
1 fork
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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Overview
Collaborative Segmentation Software
A browser-based online annotation tool for 3D medical image volumes that allow annotations to be shared between users. The sharing feature allows images to be viewed across multiple users concurrently, and can sync viewing perspectives and drawings. For a shared viewing experience, changes made to a volume/image are updated automatically when a drawing is finished or a slice is changed.
The software utilizes Pusher, which eliminates the need for a server to handle real-time functionality.
Website
Documentation
Technologies
Features
The software contains 3 types of synchronization features for easy collaboration:
  • Annotation Sync



  • Perspective View Sync



  • Slice View Sync



  • Simple UI



Loading Medical Volumes
Settings & Controls
FunctionsDescription
Select ColorChanges the color of the pen used to draw annotations
Toggle DrawingEnables and disables the use of the pen
Toggle ErasingEnables and disables the use of the eraser
Change ViewChanges the canvas to display different perspectives of the 3D medical image
UndoRemoves the latest annotation created
Save .nvdSaves the medical image with annotations, can be uploaded to re-annotate
Save .niiSaves the annotations only
Save .pngSaves the current image slice with annotations
Opacity SliderChanges opacity of the annotations: 0 - Clear, 1 - Opaque
Slice CycleChanges the canvas to display different slices of the 3D medical image
ZoomMove closer or further from the canvas
MeasureMeasures length from the starting to ending point with units in millimeters
Sync ViewEnables and disables both annotation and image view sync
Supported Images
FormatsFile Type
VoxelNIfTI, NRRD, MRtrix MIF, AFNI HEAD/BRIK, MGH/MGZ, ITK MHD, ECAT7
MeshGIfTI, ASC, BrainSuite DFS, PLY, BrainNet NV, BrainVoyager SRF, FreeSurfer, MZ3, OFF, Wavefront OBJ, STL, Legacy VTK, X3D
Mesh OverlayGIfTI, CIfTI-2, MZ3, SMP, STC, FreeSurfer (CURV/ANNOT)
TractographyTCK, TRK, TRX, VTK, AFNI .niml.tract
DICOMDICOM, DICOM Manifests


About
A project from CS 410 (Intro to Software Engineering) for Massachusetts General Hospital
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