Installation

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Michael Innerberger edited this page Dec 15, 2023 · 3 revisions

Using Conda (all platforms)

We recommend using Conda to install STIM. If you don't have Conda installed, please follow the instructions here. Once Conda is installed, you can install STIM from conda-forge by running:

conda install -c conda-forge stim

Building from source (Ubuntu / Linux)

Building STIM from source requires maven and OpenJDK8 (or newer). On Ubuntu, you can install them via the default package manager:

sudo apt-get install openjdk-8-jdk maven

Next, please check out this repository and go into the folder

git clone https://github.com/PreibischLab/stim.git
cd stim

The recommended way is to just call the install script without any arguments to install STIM into the checked out directory:

./install

To install into your favorite local binary $PATH (e.g., $HOME/bin) you can call:

./install $HOME/bin

All dependencies will be downloaded and managed by maven automatically. For linux-based platforms other than Ubuntu (including Mac), the process should be very similar.

This currently installs several tools: st-resave, st-add-slice, st-normalize, st-explorer, st-render, st-bdv-view, st-add-annotations, st-align-pairs, st-align-pairs-view, st-align-global.

The process should finish with a message similar to this (here we only called ./install thus installing in the code directory):

Installing 'st-explorer'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-render'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-bdv-view'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-resave'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-add-slice'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-normalize'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-add-annotations'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-pairs'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-pairs-view'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-global'command into /Users/spreibi/Downloads/stim_test/stim
Installation directory equals current directory, we are done.
Installation finished.

The installation should take around 1 minute.

Building from source (Windows)

Building STIM from source requires maven and OpenJDK8 (or newer). On Windows, we recommend to install them via conda:

conda install -c conda-forge maven openjdk

Next, please check out this repository and go into the folder

git clone https://github.com/PreibischLab/stim.git
cd stim

The recommended way is to just call the install script without any arguments to install STIM into the checked out directory:

install_windows.bat

To install into your favorite local binary %PATH% (e.g., %HOME%\bin) you can call:

install_windows.bat %HOME%\bin

From this point on, the process is the same as on Ubuntu / Linux.

Clone this wiki locally

, '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
Installation
Jump to bottom

Michael Innerberger edited this page Dec 15, 2023
·
3 revisions
Using Conda (all platforms)
We recommend using Conda to install STIM. If you don't have Conda installed, please follow the instructions here. Once Conda is installed, you can install STIM from conda-forge by running:
conda install -c conda-forge stim
Building from source (Ubuntu / Linux)
Building STIM from source requires maven and OpenJDK8 (or newer). On Ubuntu, you can install them via the default package manager:
sudo apt-get install openjdk-8-jdk maven
Next, please check out this repository and go into the folder
git clone https://github.com/PreibischLab/stim.git
cd stim

The recommended way is to just call the install script without any arguments to install STIM into the checked out directory:
./install
To install into your favorite local binary $PATH (e.g., $HOME/bin) you can call:
./install $HOME/bin
All dependencies will be downloaded and managed by maven automatically.
For linux-based platforms other than Ubuntu (including Mac), the process should be very similar.
This currently installs several tools: st-resave, st-add-slice, st-normalize, st-explorer, st-render, st-bdv-view, st-add-annotations, st-align-pairs, st-align-pairs-view, st-align-global.
The process should finish with a message similar to this (here we only called ./install thus installing in the code directory):
Installing 'st-explorer'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-render'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-bdv-view'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-resave'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-add-slice'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-normalize'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-add-annotations'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-pairs'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-pairs-view'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-global'command into /Users/spreibi/Downloads/stim_test/stim
Installation directory equals current directory, we are done.
Installation finished.
The installation should take around 1 minute.
Building from source (Windows)
Building STIM from source requires maven and OpenJDK8 (or newer). On Windows, we recommend to install them via conda:
conda install -c conda-forge maven openjdk
Next, please check out this repository and go into the folder
git clone https://github.com/PreibischLab/stim.git
cd stim

The recommended way is to just call the install script without any arguments to install STIM into the checked out directory:
install_windows.bat
To install into your favorite local binary %PATH% (e.g., %HOME%\bin) you can call:
install_windows.bat %HOME%\bin
From this point on, the process is the same as on Ubuntu / Linux.
Clone this wiki locally

, '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
Installation
Jump to bottom

Michael Innerberger edited this page Dec 15, 2023
·
3 revisions
Using Conda (all platforms)
We recommend using Conda to install STIM. If you don't have Conda installed, please follow the instructions here. Once Conda is installed, you can install STIM from conda-forge by running:
conda install -c conda-forge stim
Building from source (Ubuntu / Linux)
Building STIM from source requires maven and OpenJDK8 (or newer). On Ubuntu, you can install them via the default package manager:
sudo apt-get install openjdk-8-jdk maven
Next, please check out this repository and go into the folder
git clone https://github.com/PreibischLab/stim.git
cd stim

The recommended way is to just call the install script without any arguments to install STIM into the checked out directory:
./install
To install into your favorite local binary $PATH (e.g., $HOME/bin) you can call:
./install $HOME/bin
All dependencies will be downloaded and managed by maven automatically.
For linux-based platforms other than Ubuntu (including Mac), the process should be very similar.
This currently installs several tools: st-resave, st-add-slice, st-normalize, st-explorer, st-render, st-bdv-view, st-add-annotations, st-align-pairs, st-align-pairs-view, st-align-global.
The process should finish with a message similar to this (here we only called ./install thus installing in the code directory):
Installing 'st-explorer'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-render'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-bdv-view'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-resave'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-add-slice'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-normalize'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-add-annotations'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-pairs'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-pairs-view'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-global'command into /Users/spreibi/Downloads/stim_test/stim
Installation directory equals current directory, we are done.
Installation finished.
The installation should take around 1 minute.
Building from source (Windows)
Building STIM from source requires maven and OpenJDK8 (or newer). On Windows, we recommend to install them via conda:
conda install -c conda-forge maven openjdk
Next, please check out this repository and go into the folder
git clone https://github.com/PreibischLab/stim.git
cd stim

The recommended way is to just call the install script without any arguments to install STIM into the checked out directory:
install_windows.bat
To install into your favorite local binary %PATH% (e.g., %HOME%\bin) you can call:
install_windows.bat %HOME%\bin
From this point on, the process is the same as on Ubuntu / Linux.
Clone this wiki locally

, '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
Installation
Jump to bottom

Michael Innerberger edited this page Dec 15, 2023
·
3 revisions
Using Conda (all platforms)
We recommend using Conda to install STIM. If you don't have Conda installed, please follow the instructions here. Once Conda is installed, you can install STIM from conda-forge by running:
conda install -c conda-forge stim
Building from source (Ubuntu / Linux)
Building STIM from source requires maven and OpenJDK8 (or newer). On Ubuntu, you can install them via the default package manager:
sudo apt-get install openjdk-8-jdk maven
Next, please check out this repository and go into the folder
git clone https://github.com/PreibischLab/stim.git
cd stim

The recommended way is to just call the install script without any arguments to install STIM into the checked out directory:
./install
To install into your favorite local binary $PATH (e.g., $HOME/bin) you can call:
./install $HOME/bin
All dependencies will be downloaded and managed by maven automatically.
For linux-based platforms other than Ubuntu (including Mac), the process should be very similar.
This currently installs several tools: st-resave, st-add-slice, st-normalize, st-explorer, st-render, st-bdv-view, st-add-annotations, st-align-pairs, st-align-pairs-view, st-align-global.
The process should finish with a message similar to this (here we only called ./install thus installing in the code directory):
Installing 'st-explorer'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-render'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-bdv-view'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-resave'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-add-slice'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-normalize'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-add-annotations'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-pairs'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-pairs-view'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-global'command into /Users/spreibi/Downloads/stim_test/stim
Installation directory equals current directory, we are done.
Installation finished.
The installation should take around 1 minute.
Building from source (Windows)
Building STIM from source requires maven and OpenJDK8 (or newer). On Windows, we recommend to install them via conda:
conda install -c conda-forge maven openjdk
Next, please check out this repository and go into the folder
git clone https://github.com/PreibischLab/stim.git
cd stim

The recommended way is to just call the install script without any arguments to install STIM into the checked out directory:
install_windows.bat
To install into your favorite local binary %PATH% (e.g., %HOME%\bin) you can call:
install_windows.bat %HOME%\bin
From this point on, the process is the same as on Ubuntu / Linux.
Clone this wiki locally

, '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
Installation
Jump to bottom

Michael Innerberger edited this page Dec 15, 2023
·
3 revisions
Using Conda (all platforms)
We recommend using Conda to install STIM. If you don't have Conda installed, please follow the instructions here. Once Conda is installed, you can install STIM from conda-forge by running:
conda install -c conda-forge stim
Building from source (Ubuntu / Linux)
Building STIM from source requires maven and OpenJDK8 (or newer). On Ubuntu, you can install them via the default package manager:
sudo apt-get install openjdk-8-jdk maven
Next, please check out this repository and go into the folder
git clone https://github.com/PreibischLab/stim.git
cd stim

The recommended way is to just call the install script without any arguments to install STIM into the checked out directory:
./install
To install into your favorite local binary $PATH (e.g., $HOME/bin) you can call:
./install $HOME/bin
All dependencies will be downloaded and managed by maven automatically.
For linux-based platforms other than Ubuntu (including Mac), the process should be very similar.
This currently installs several tools: st-resave, st-add-slice, st-normalize, st-explorer, st-render, st-bdv-view, st-add-annotations, st-align-pairs, st-align-pairs-view, st-align-global.
The process should finish with a message similar to this (here we only called ./install thus installing in the code directory):
Installing 'st-explorer'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-render'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-bdv-view'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-resave'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-add-slice'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-normalize'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-add-annotations'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-pairs'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-pairs-view'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-global'command into /Users/spreibi/Downloads/stim_test/stim
Installation directory equals current directory, we are done.
Installation finished.
The installation should take around 1 minute.
Building from source (Windows)
Building STIM from source requires maven and OpenJDK8 (or newer). On Windows, we recommend to install them via conda:
conda install -c conda-forge maven openjdk
Next, please check out this repository and go into the folder
git clone https://github.com/PreibischLab/stim.git
cd stim

The recommended way is to just call the install script without any arguments to install STIM into the checked out directory:
install_windows.bat
To install into your favorite local binary %PATH% (e.g., %HOME%\bin) you can call:
install_windows.bat %HOME%\bin
From this point on, the process is the same as on Ubuntu / Linux.
Clone this wiki locally

, '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
Installation
Jump to bottom

Michael Innerberger edited this page Dec 15, 2023
·
3 revisions
Using Conda (all platforms)
We recommend using Conda to install STIM. If you don't have Conda installed, please follow the instructions here. Once Conda is installed, you can install STIM from conda-forge by running:
conda install -c conda-forge stim
Building from source (Ubuntu / Linux)
Building STIM from source requires maven and OpenJDK8 (or newer). On Ubuntu, you can install them via the default package manager:
sudo apt-get install openjdk-8-jdk maven
Next, please check out this repository and go into the folder
git clone https://github.com/PreibischLab/stim.git
cd stim

The recommended way is to just call the install script without any arguments to install STIM into the checked out directory:
./install
To install into your favorite local binary $PATH (e.g., $HOME/bin) you can call:
./install $HOME/bin
All dependencies will be downloaded and managed by maven automatically.
For linux-based platforms other than Ubuntu (including Mac), the process should be very similar.
This currently installs several tools: st-resave, st-add-slice, st-normalize, st-explorer, st-render, st-bdv-view, st-add-annotations, st-align-pairs, st-align-pairs-view, st-align-global.
The process should finish with a message similar to this (here we only called ./install thus installing in the code directory):
Installing 'st-explorer'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-render'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-bdv-view'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-resave'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-add-slice'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-normalize'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-add-annotations'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-pairs'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-pairs-view'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-global'command into /Users/spreibi/Downloads/stim_test/stim
Installation directory equals current directory, we are done.
Installation finished.
The installation should take around 1 minute.
Building from source (Windows)
Building STIM from source requires maven and OpenJDK8 (or newer). On Windows, we recommend to install them via conda:
conda install -c conda-forge maven openjdk
Next, please check out this repository and go into the folder
git clone https://github.com/PreibischLab/stim.git
cd stim

The recommended way is to just call the install script without any arguments to install STIM into the checked out directory:
install_windows.bat
To install into your favorite local binary %PATH% (e.g., %HOME%\bin) you can call:
install_windows.bat %HOME%\bin
From this point on, the process is the same as on Ubuntu / Linux.
Clone this wiki locally

, '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
Installation
Jump to bottom

Michael Innerberger edited this page Dec 15, 2023
·
3 revisions
Using Conda (all platforms)
We recommend using Conda to install STIM. If you don't have Conda installed, please follow the instructions here. Once Conda is installed, you can install STIM from conda-forge by running:
conda install -c conda-forge stim
Building from source (Ubuntu / Linux)
Building STIM from source requires maven and OpenJDK8 (or newer). On Ubuntu, you can install them via the default package manager:
sudo apt-get install openjdk-8-jdk maven
Next, please check out this repository and go into the folder
git clone https://github.com/PreibischLab/stim.git
cd stim

The recommended way is to just call the install script without any arguments to install STIM into the checked out directory:
./install
To install into your favorite local binary $PATH (e.g., $HOME/bin) you can call:
./install $HOME/bin
All dependencies will be downloaded and managed by maven automatically.
For linux-based platforms other than Ubuntu (including Mac), the process should be very similar.
This currently installs several tools: st-resave, st-add-slice, st-normalize, st-explorer, st-render, st-bdv-view, st-add-annotations, st-align-pairs, st-align-pairs-view, st-align-global.
The process should finish with a message similar to this (here we only called ./install thus installing in the code directory):
Installing 'st-explorer'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-render'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-bdv-view'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-resave'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-add-slice'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-normalize'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-add-annotations'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-pairs'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-pairs-view'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-global'command into /Users/spreibi/Downloads/stim_test/stim
Installation directory equals current directory, we are done.
Installation finished.
The installation should take around 1 minute.
Building from source (Windows)
Building STIM from source requires maven and OpenJDK8 (or newer). On Windows, we recommend to install them via conda:
conda install -c conda-forge maven openjdk
Next, please check out this repository and go into the folder
git clone https://github.com/PreibischLab/stim.git
cd stim

The recommended way is to just call the install script without any arguments to install STIM into the checked out directory:
install_windows.bat
To install into your favorite local binary %PATH% (e.g., %HOME%\bin) you can call:
install_windows.bat %HOME%\bin
From this point on, the process is the same as on Ubuntu / Linux.
Clone this wiki locally

, '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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Michael Innerberger edited this page Dec 15, 2023
·
3 revisions
Using Conda (all platforms)
We recommend using Conda to install STIM. If you don't have Conda installed, please follow the instructions here. Once Conda is installed, you can install STIM from conda-forge by running:
conda install -c conda-forge stim
Building from source (Ubuntu / Linux)
Building STIM from source requires maven and OpenJDK8 (or newer). On Ubuntu, you can install them via the default package manager:
sudo apt-get install openjdk-8-jdk maven
Next, please check out this repository and go into the folder
git clone https://github.com/PreibischLab/stim.git
cd stim

The recommended way is to just call the install script without any arguments to install STIM into the checked out directory:
./install
To install into your favorite local binary $PATH (e.g., $HOME/bin) you can call:
./install $HOME/bin
All dependencies will be downloaded and managed by maven automatically.
For linux-based platforms other than Ubuntu (including Mac), the process should be very similar.
This currently installs several tools: st-resave, st-add-slice, st-normalize, st-explorer, st-render, st-bdv-view, st-add-annotations, st-align-pairs, st-align-pairs-view, st-align-global.
The process should finish with a message similar to this (here we only called ./install thus installing in the code directory):
Installing 'st-explorer'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-render'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-bdv-view'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-resave'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-add-slice'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-normalize'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-add-annotations'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-pairs'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-pairs-view'command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-global'command into /Users/spreibi/Downloads/stim_test/stim
Installation directory equals current directory, we are done.
Installation finished.
The installation should take around 1 minute.
Building from source (Windows)
Building STIM from source requires maven and OpenJDK8 (or newer). On Windows, we recommend to install them via conda:
conda install -c conda-forge maven openjdk
Next, please check out this repository and go into the folder
git clone https://github.com/PreibischLab/stim.git
cd stim

The recommended way is to just call the install script without any arguments to install STIM into the checked out directory:
install_windows.bat
To install into your favorite local binary %PATH% (e.g., %HOME%\bin) you can call:
install_windows.bat %HOME%\bin
From this point on, the process is the same as on Ubuntu / Linux.
Clone this wiki locally