@Digital-Pathology

Digital-Pathology

README.md

DigitalPathology

This repo has multiple tools, utilities, and sub-projects that the 2021-2022 Digital Pathology team worked on throughout their senior design series. The material in this repo was largely designed for use on AWS Sagemaker.

CustomDatasets

Note: This requires using OpenSlideStartupScript for use on AWS Sagemaker Studio.

This is a module for use with PyTorch's models - it offers an interface for accessing very large tif biomedical slides stored on S3. Please see ExampleCustomDatasetUse.ipynb for details on the use of this module.

It was developed using the following resources:

OpenSlideStartupScript

This script is for use as a Python instance startup script on AWS Sagemaker Studio Python Notebooks. With respect to using them in development, select the aptly-named startup script upon initializing your notebook instances "adins-test-startup-thing". This is necessary for using OpenSlide, a requirement for using CustomDatasets.

Pinned Loading

  1. CustomDatasetCustomDatasetPublic

    Python

  2. ML-UnsupervisedML-UnsupervisedPublic

    Jupyter Notebook

  3. ML-SupervisedML-SupervisedPublic

    Python

  4. UnifiedImageReaderUnifiedImageReaderPublic

    Python 1

  5. SagemakerNotebookSagemakerNotebookPublic

    Jupyter Notebook

  6. SagemakerTemplateSagemakerTemplatePublic

    Shell

Repositories

Showing 10 of 15 repositories
View all repositories

Top languages

Loading…

Most used topics

Loading…

, '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
@Digital-Pathology

Digital-Pathology

README.md
DigitalPathology
This repo has multiple tools, utilities, and sub-projects that the 2021-2022 Digital Pathology team worked on throughout their senior design series. The material in this repo was largely designed for use on AWS Sagemaker.
CustomDatasets
Note: This requires using OpenSlideStartupScript for use on AWS Sagemaker Studio.
This is a module for use with PyTorch's models - it offers an interface for accessing very large tif biomedical slides stored on S3. Please see ExampleCustomDatasetUse.ipynb for details on the use of this module.
It was developed using the following resources:
OpenSlideStartupScript
This script is for use as a Python instance startup script on AWS Sagemaker Studio Python Notebooks. With respect to using them in development, select the aptly-named startup script upon initializing your notebook instances "adins-test-startup-thing". This is necessary for using OpenSlide, a requirement for using CustomDatasets.

Pinned
Loading
  1. CustomDatasetCustomDatasetPublic
    Python
  2. ML-UnsupervisedML-UnsupervisedPublic
    Jupyter Notebook
  3. ML-SupervisedML-SupervisedPublic
    Python
  4. UnifiedImageReaderUnifiedImageReaderPublic
    Python
1

  5. SagemakerNotebookSagemakerNotebookPublic
    Jupyter Notebook
  6. SagemakerTemplateSagemakerTemplatePublic
    Shell

Repositories

Showing 10 of 15 repositories
View all repositories
Top languages
Loading…
Most used topics
Loading…

, '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
@Digital-Pathology

Digital-Pathology

README.md
DigitalPathology
This repo has multiple tools, utilities, and sub-projects that the 2021-2022 Digital Pathology team worked on throughout their senior design series. The material in this repo was largely designed for use on AWS Sagemaker.
CustomDatasets
Note: This requires using OpenSlideStartupScript for use on AWS Sagemaker Studio.
This is a module for use with PyTorch's models - it offers an interface for accessing very large tif biomedical slides stored on S3. Please see ExampleCustomDatasetUse.ipynb for details on the use of this module.
It was developed using the following resources:
OpenSlideStartupScript
This script is for use as a Python instance startup script on AWS Sagemaker Studio Python Notebooks. With respect to using them in development, select the aptly-named startup script upon initializing your notebook instances "adins-test-startup-thing". This is necessary for using OpenSlide, a requirement for using CustomDatasets.

Pinned
Loading
  1. CustomDatasetCustomDatasetPublic
    Python
  2. ML-UnsupervisedML-UnsupervisedPublic
    Jupyter Notebook
  3. ML-SupervisedML-SupervisedPublic
    Python
  4. UnifiedImageReaderUnifiedImageReaderPublic
    Python
1

  5. SagemakerNotebookSagemakerNotebookPublic
    Jupyter Notebook
  6. SagemakerTemplateSagemakerTemplatePublic
    Shell

Repositories

Showing 10 of 15 repositories
View all repositories
Top languages
Loading…
Most used topics
Loading…

, '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
@Digital-Pathology

Digital-Pathology

README.md
DigitalPathology
This repo has multiple tools, utilities, and sub-projects that the 2021-2022 Digital Pathology team worked on throughout their senior design series. The material in this repo was largely designed for use on AWS Sagemaker.
CustomDatasets
Note: This requires using OpenSlideStartupScript for use on AWS Sagemaker Studio.
This is a module for use with PyTorch's models - it offers an interface for accessing very large tif biomedical slides stored on S3. Please see ExampleCustomDatasetUse.ipynb for details on the use of this module.
It was developed using the following resources:
OpenSlideStartupScript
This script is for use as a Python instance startup script on AWS Sagemaker Studio Python Notebooks. With respect to using them in development, select the aptly-named startup script upon initializing your notebook instances "adins-test-startup-thing". This is necessary for using OpenSlide, a requirement for using CustomDatasets.

Pinned
Loading
  1. CustomDatasetCustomDatasetPublic
    Python
  2. ML-UnsupervisedML-UnsupervisedPublic
    Jupyter Notebook
  3. ML-SupervisedML-SupervisedPublic
    Python
  4. UnifiedImageReaderUnifiedImageReaderPublic
    Python
1

  5. SagemakerNotebookSagemakerNotebookPublic
    Jupyter Notebook
  6. SagemakerTemplateSagemakerTemplatePublic
    Shell

Repositories

Showing 10 of 15 repositories
View all repositories
Top languages
Loading…
Most used topics
Loading…

, '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
@Digital-Pathology

Digital-Pathology

README.md
DigitalPathology
This repo has multiple tools, utilities, and sub-projects that the 2021-2022 Digital Pathology team worked on throughout their senior design series. The material in this repo was largely designed for use on AWS Sagemaker.
CustomDatasets
Note: This requires using OpenSlideStartupScript for use on AWS Sagemaker Studio.
This is a module for use with PyTorch's models - it offers an interface for accessing very large tif biomedical slides stored on S3. Please see ExampleCustomDatasetUse.ipynb for details on the use of this module.
It was developed using the following resources:
OpenSlideStartupScript
This script is for use as a Python instance startup script on AWS Sagemaker Studio Python Notebooks. With respect to using them in development, select the aptly-named startup script upon initializing your notebook instances "adins-test-startup-thing". This is necessary for using OpenSlide, a requirement for using CustomDatasets.

Pinned
Loading
  1. CustomDatasetCustomDatasetPublic
    Python
  2. ML-UnsupervisedML-UnsupervisedPublic
    Jupyter Notebook
  3. ML-SupervisedML-SupervisedPublic
    Python
  4. UnifiedImageReaderUnifiedImageReaderPublic
    Python
1

  5. SagemakerNotebookSagemakerNotebookPublic
    Jupyter Notebook
  6. SagemakerTemplateSagemakerTemplatePublic
    Shell

Repositories

Showing 10 of 15 repositories
View all repositories
Top languages
Loading…
Most used topics
Loading…

, '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
@Digital-Pathology

Digital-Pathology

README.md
DigitalPathology
This repo has multiple tools, utilities, and sub-projects that the 2021-2022 Digital Pathology team worked on throughout their senior design series. The material in this repo was largely designed for use on AWS Sagemaker.
CustomDatasets
Note: This requires using OpenSlideStartupScript for use on AWS Sagemaker Studio.
This is a module for use with PyTorch's models - it offers an interface for accessing very large tif biomedical slides stored on S3. Please see ExampleCustomDatasetUse.ipynb for details on the use of this module.
It was developed using the following resources:
OpenSlideStartupScript
This script is for use as a Python instance startup script on AWS Sagemaker Studio Python Notebooks. With respect to using them in development, select the aptly-named startup script upon initializing your notebook instances "adins-test-startup-thing". This is necessary for using OpenSlide, a requirement for using CustomDatasets.

Pinned
Loading
  1. CustomDatasetCustomDatasetPublic
    Python
  2. ML-UnsupervisedML-UnsupervisedPublic
    Jupyter Notebook
  3. ML-SupervisedML-SupervisedPublic
    Python
  4. UnifiedImageReaderUnifiedImageReaderPublic
    Python
1

  5. SagemakerNotebookSagemakerNotebookPublic
    Jupyter Notebook
  6. SagemakerTemplateSagemakerTemplatePublic
    Shell

Repositories

Showing 10 of 15 repositories
View all repositories
Top languages
Loading…
Most used topics
Loading…

, '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
@Digital-Pathology

Digital-Pathology

README.md
DigitalPathology
This repo has multiple tools, utilities, and sub-projects that the 2021-2022 Digital Pathology team worked on throughout their senior design series. The material in this repo was largely designed for use on AWS Sagemaker.
CustomDatasets
Note: This requires using OpenSlideStartupScript for use on AWS Sagemaker Studio.
This is a module for use with PyTorch's models - it offers an interface for accessing very large tif biomedical slides stored on S3. Please see ExampleCustomDatasetUse.ipynb for details on the use of this module.
It was developed using the following resources:
OpenSlideStartupScript
This script is for use as a Python instance startup script on AWS Sagemaker Studio Python Notebooks. With respect to using them in development, select the aptly-named startup script upon initializing your notebook instances "adins-test-startup-thing". This is necessary for using OpenSlide, a requirement for using CustomDatasets.

Pinned
Loading
  1. CustomDatasetCustomDatasetPublic
    Python
  2. ML-UnsupervisedML-UnsupervisedPublic
    Jupyter Notebook
  3. ML-SupervisedML-SupervisedPublic
    Python
  4. UnifiedImageReaderUnifiedImageReaderPublic
    Python
1

  5. SagemakerNotebookSagemakerNotebookPublic
    Jupyter Notebook
  6. SagemakerTemplateSagemakerTemplatePublic
    Shell

Repositories

Showing 10 of 15 repositories
View all repositories
Top languages
Loading…
Most used topics
Loading…

, '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); }
})();
})();

Skip to content
@Digital-Pathology

Digital-Pathology

README.md
DigitalPathology
This repo has multiple tools, utilities, and sub-projects that the 2021-2022 Digital Pathology team worked on throughout their senior design series. The material in this repo was largely designed for use on AWS Sagemaker.
CustomDatasets
Note: This requires using OpenSlideStartupScript for use on AWS Sagemaker Studio.
This is a module for use with PyTorch's models - it offers an interface for accessing very large tif biomedical slides stored on S3. Please see ExampleCustomDatasetUse.ipynb for details on the use of this module.
It was developed using the following resources:
OpenSlideStartupScript
This script is for use as a Python instance startup script on AWS Sagemaker Studio Python Notebooks. With respect to using them in development, select the aptly-named startup script upon initializing your notebook instances "adins-test-startup-thing". This is necessary for using OpenSlide, a requirement for using CustomDatasets.

Pinned
Loading
  1. CustomDatasetCustomDatasetPublic
    Python
  2. ML-UnsupervisedML-UnsupervisedPublic
    Jupyter Notebook
  3. ML-SupervisedML-SupervisedPublic
    Python
  4. UnifiedImageReaderUnifiedImageReaderPublic
    Python
1

  5. SagemakerNotebookSagemakerNotebookPublic
    Jupyter Notebook
  6. SagemakerTemplateSagemakerTemplatePublic
    Shell

Repositories

Showing 10 of 15 repositories
View all repositories
Top languages
Loading…
Most used topics
Loading…