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wsic

Gitmojiimageimage

Python applicationDocumentation Status

imageimageimage

Whole Slide Image (WSI) conversion for brightfield histology images.

Provides a command line interface (CLI) for easy convertion between formats:

Usage: wsic convert [OPTIONS]
Convert a WSI.
Options:
-i, --in-path PATH Path to WSI to read from.
-o, --out-path PATH The path to output to.
-t, --tile-size <INTEGER INTEGER>...
The size of the tiles to write.
-rt, --read-tile-size <INTEGER INTEGER>...
The size of the tiles to read.
-w, --workers INTEGER The number of workers to use.
-c, --compression [blosc|deflate|jpeg xl|jpeg-ls|jpeg|jpeg2000|lzw|png|webp|zstd]
The compression to use.
-cl, --compression-level INTEGER
The compression level to use.
-d, --downsample INTEGER The downsample factor to use.
-mpp, --microns-per-pixel <FLOAT FLOAT>...
The microns per pixel to use.
-ome, --ome / --no-ome Save with OME-TIFF metadata (OME-TIFF and
NGFF).
--overwrite / --no-overwrite Whether to overwrite the output file.
-to, --timeout FLOAT Timeout in seconds for reading a tile.
-W, --writer [auto|jp2|svs|tiff|zarr]
The writer to use. Overrides writer detected
by output file extension.
-s, --store [dir|ndir|zip|sqlite]
The store to use (zarr/NGFF only). Defaults
to ndir (nested directory).
-h, --help Show this message and exit.

A demonstration of converting a JP2 file to a pyramid TIFF.

Getting Started

For basic usage see the documentation page "How do I...?".

Features

  • Reading and writing several container formats.
  • Support for a wide range of compression codecs.
  • Custom tile size
  • Lossless repackaging / transcoding (to zarr/NGFF or TIFF) from:
    • SVS (JPEG compressed)
    • OME-TIFF (single image, JPEG and JPEG2000 (J2K) compressed)
    • Generic Tiled TIFF (JPEG, JPEG2000, and WebP compressed)
    • DICOM WSI (JPEG and JPEG2000 (J2K) compressed)

Read Container Formats

  • OpenSlide Formats:
    • Aperio SVS (.svs)
    • Hamamatsu (.vms, .vmu, .ndpi)
    • Leica (.scn)
    • Mirax MRXS (.mrxs)
    • Sakura (.svslide)
    • Trestle (.tif)
    • Ventana (.bif, .tif)
    • Generic tiled TIFF (.tif; DEFLATE, JPEG, and Webp compressed)
  • Other Tiled TIFFs (tifffile supported formats)
    • Tiled with various codecs: e.g. JPEG XL, JPEG 2000, WebP, and zstd.
    • RGB/brightfield OME-TIFF.
  • JP2 (via glymur and OpenJPEG)
    • Including Omnyx JP2 files.
  • Zarr
    • Single array.
    • Group of (multiresolution) arrays.
    • NGFF v0.4.
  • DICOM WSI (via wsidicom)

Write Container Formats

  • TIFF
    • Generic Tiled / Pyramid TIFF
    • OME-TIFF
    • SVS
  • JP2
  • Zarr (NGFF v0.4)
  • DICOM (.dcm)

Notes & FAQs

Python on Windows handles multiprocessing differenly to POSIX/UNIX-like systems. I suggest using the Windows Subsystem for Linux on Windows to ensure that wsic functions correctly and efficiently.

Other Tools

There are many other great tools in this space. Below are some other tools for converting WSIs.

  1. bfconvert Part of the Bio-Formats command line tools. Uses bioformats to convert from many formats to OME-TIFF.
  2. biofromats2raw Convert from Bio-Formats formats to zarr.
  3. isyntax2raw Convert from Philips' iSyntax format to a zarr using Philips' SDK.
  4. wsidicomiser Convert OpenSlide images to WSI DICOM.

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

About

Whole Slide image (WSI) conversion for brightfield histology images

Resources

Readme
License

Contributing

Contributing
Activity
Custom properties

Stars

1 star

Watchers

0 watching

Forks

0 forks
Report repository

Releases

Packages

Contributors

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
wsic
Gitmojiimageimage
Python applicationDocumentation Status
imageimageimage
Whole Slide Image (WSI) conversion for brightfield histology images.
Provides a command line interface (CLI) for easy convertion between
formats:
Usage: wsic convert [OPTIONS]
Convert a WSI.
Options:
-i, --in-path PATH Path to WSI to read from.
-o, --out-path PATH The path to output to.
-t, --tile-size <INTEGER INTEGER>...
The size of the tiles to write.
-rt, --read-tile-size <INTEGER INTEGER>...
The size of the tiles to read.
-w, --workers INTEGER The number of workers to use.
-c, --compression [blosc|deflate|jpeg xl|jpeg-ls|jpeg|jpeg2000|lzw|png|webp|zstd]
The compression to use.
-cl, --compression-level INTEGER
The compression level to use.
-d, --downsample INTEGER The downsample factor to use.
-mpp, --microns-per-pixel <FLOAT FLOAT>...
The microns per pixel to use.
-ome, --ome / --no-ome Save with OME-TIFF metadata (OME-TIFF and
NGFF).
--overwrite / --no-overwrite Whether to overwrite the output file.
-to, --timeout FLOAT Timeout in seconds for reading a tile.
-W, --writer [auto|jp2|svs|tiff|zarr]
The writer to use. Overrides writer detected
by output file extension.
-s, --store [dir|ndir|zip|sqlite]
The store to use (zarr/NGFF only). Defaults
to ndir (nested directory).
-h, --help Show this message and exit.

A demonstration of converting a JP2 file to a pyramid TIFF.
Getting Started
For basic usage see the documentation page "How do
I...?".
Features
  • Reading and writing several container formats.
  • Support for a wide range of compression codecs.
  • Custom tile size
  • Lossless repackaging / transcoding (to zarr/NGFF or TIFF) from:

    • SVS (JPEG compressed)
    • OME-TIFF (single image, JPEG and JPEG2000 (J2K) compressed)
    • Generic Tiled TIFF (JPEG, JPEG2000, and WebP compressed)
    • DICOM WSI (JPEG and JPEG2000 (J2K) compressed)
Read Container Formats
  • OpenSlide Formats:

    • Aperio SVS (.svs)
    • Hamamatsu (.vms, .vmu, .ndpi)
    • Leica (.scn)
    • Mirax MRXS (.mrxs)
    • Sakura (.svslide)
    • Trestle (.tif)
    • Ventana (.bif, .tif)
    • Generic tiled TIFF (.tif; DEFLATE, JPEG, and Webp
compressed)
  • Other Tiled TIFFs
(tifffile supported
formats)

    • Tiled with various codecs: e.g. JPEG XL, JPEG 2000, WebP, and zstd.
    • RGB/brightfield OME-TIFF.
  • JP2 (via
glymur and
OpenJPEG)

    • Including Omnyx JP2 files.
  • Zarr
    • Single array.
    • Group of (multiresolution) arrays.
    • NGFF v0.4.
  • DICOM WSI (via
wsidicom)

Write Container Formats
  • TIFF

    • Generic Tiled / Pyramid TIFF
    • OME-TIFF
    • SVS
  • JP2
  • Zarr (NGFF v0.4)
  • DICOM (.dcm)
Notes & FAQs
Python on Windows handles multiprocessing
differenly
to POSIX/UNIX-like systems. I suggest using the Windows Subsystem for
Linux on Windows
to ensure that wsic functions correctly and efficiently.
Other Tools
There are many other great tools in this space. Below are some other
tools for converting WSIs.
  1. bfconvert
Part of the Bio-Formats command line tools. Uses bioformats to convert
from many formats to OME-TIFF.
  2. biofromats2raw
Convert from Bio-Formats formats to zarr.
  3. isyntax2raw Convert from Philips' iSyntax format to a zarr using Philips' SDK.
  4. wsidicomiser Convert OpenSlide images to WSI DICOM.
Credits
This package was created with
Cookiecutter and the
audreyr/cookiecutter-pypackage
project template.
About
Whole Slide image (WSI) conversion for brightfield histology images
Resources
Readme
License
Contributing
Contributing
Activity
Custom properties
Stars
1 star
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
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
wsic
Gitmojiimageimage
Python applicationDocumentation Status
imageimageimage
Whole Slide Image (WSI) conversion for brightfield histology images.
Provides a command line interface (CLI) for easy convertion between
formats:
Usage: wsic convert [OPTIONS]
Convert a WSI.
Options:
-i, --in-path PATH Path to WSI to read from.
-o, --out-path PATH The path to output to.
-t, --tile-size <INTEGER INTEGER>...
The size of the tiles to write.
-rt, --read-tile-size <INTEGER INTEGER>...
The size of the tiles to read.
-w, --workers INTEGER The number of workers to use.
-c, --compression [blosc|deflate|jpeg xl|jpeg-ls|jpeg|jpeg2000|lzw|png|webp|zstd]
The compression to use.
-cl, --compression-level INTEGER
The compression level to use.
-d, --downsample INTEGER The downsample factor to use.
-mpp, --microns-per-pixel <FLOAT FLOAT>...
The microns per pixel to use.
-ome, --ome / --no-ome Save with OME-TIFF metadata (OME-TIFF and
NGFF).
--overwrite / --no-overwrite Whether to overwrite the output file.
-to, --timeout FLOAT Timeout in seconds for reading a tile.
-W, --writer [auto|jp2|svs|tiff|zarr]
The writer to use. Overrides writer detected
by output file extension.
-s, --store [dir|ndir|zip|sqlite]
The store to use (zarr/NGFF only). Defaults
to ndir (nested directory).
-h, --help Show this message and exit.

A demonstration of converting a JP2 file to a pyramid TIFF.
Getting Started
For basic usage see the documentation page "How do
I...?".
Features
  • Reading and writing several container formats.
  • Support for a wide range of compression codecs.
  • Custom tile size
  • Lossless repackaging / transcoding (to zarr/NGFF or TIFF) from:

    • SVS (JPEG compressed)
    • OME-TIFF (single image, JPEG and JPEG2000 (J2K) compressed)
    • Generic Tiled TIFF (JPEG, JPEG2000, and WebP compressed)
    • DICOM WSI (JPEG and JPEG2000 (J2K) compressed)
Read Container Formats
  • OpenSlide Formats:

    • Aperio SVS (.svs)
    • Hamamatsu (.vms, .vmu, .ndpi)
    • Leica (.scn)
    • Mirax MRXS (.mrxs)
    • Sakura (.svslide)
    • Trestle (.tif)
    • Ventana (.bif, .tif)
    • Generic tiled TIFF (.tif; DEFLATE, JPEG, and Webp
compressed)
  • Other Tiled TIFFs
(tifffile supported
formats)

    • Tiled with various codecs: e.g. JPEG XL, JPEG 2000, WebP, and zstd.
    • RGB/brightfield OME-TIFF.
  • JP2 (via
glymur and
OpenJPEG)

    • Including Omnyx JP2 files.
  • Zarr
    • Single array.
    • Group of (multiresolution) arrays.
    • NGFF v0.4.
  • DICOM WSI (via
wsidicom)

Write Container Formats
  • TIFF

    • Generic Tiled / Pyramid TIFF
    • OME-TIFF
    • SVS
  • JP2
  • Zarr (NGFF v0.4)
  • DICOM (.dcm)
Notes & FAQs
Python on Windows handles multiprocessing
differenly
to POSIX/UNIX-like systems. I suggest using the Windows Subsystem for
Linux on Windows
to ensure that wsic functions correctly and efficiently.
Other Tools
There are many other great tools in this space. Below are some other
tools for converting WSIs.
  1. bfconvert
Part of the Bio-Formats command line tools. Uses bioformats to convert
from many formats to OME-TIFF.
  2. biofromats2raw
Convert from Bio-Formats formats to zarr.
  3. isyntax2raw Convert from Philips' iSyntax format to a zarr using Philips' SDK.
  4. wsidicomiser Convert OpenSlide images to WSI DICOM.
Credits
This package was created with
Cookiecutter and the
audreyr/cookiecutter-pypackage
project template.
About
Whole Slide image (WSI) conversion for brightfield histology images
Resources
Readme
License
Contributing
Contributing
Activity
Custom properties
Stars
1 star
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
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
wsic
Gitmojiimageimage
Python applicationDocumentation Status
imageimageimage
Whole Slide Image (WSI) conversion for brightfield histology images.
Provides a command line interface (CLI) for easy convertion between
formats:
Usage: wsic convert [OPTIONS]
Convert a WSI.
Options:
-i, --in-path PATH Path to WSI to read from.
-o, --out-path PATH The path to output to.
-t, --tile-size <INTEGER INTEGER>...
The size of the tiles to write.
-rt, --read-tile-size <INTEGER INTEGER>...
The size of the tiles to read.
-w, --workers INTEGER The number of workers to use.
-c, --compression [blosc|deflate|jpeg xl|jpeg-ls|jpeg|jpeg2000|lzw|png|webp|zstd]
The compression to use.
-cl, --compression-level INTEGER
The compression level to use.
-d, --downsample INTEGER The downsample factor to use.
-mpp, --microns-per-pixel <FLOAT FLOAT>...
The microns per pixel to use.
-ome, --ome / --no-ome Save with OME-TIFF metadata (OME-TIFF and
NGFF).
--overwrite / --no-overwrite Whether to overwrite the output file.
-to, --timeout FLOAT Timeout in seconds for reading a tile.
-W, --writer [auto|jp2|svs|tiff|zarr]
The writer to use. Overrides writer detected
by output file extension.
-s, --store [dir|ndir|zip|sqlite]
The store to use (zarr/NGFF only). Defaults
to ndir (nested directory).
-h, --help Show this message and exit.

A demonstration of converting a JP2 file to a pyramid TIFF.
Getting Started
For basic usage see the documentation page "How do
I...?".
Features
  • Reading and writing several container formats.
  • Support for a wide range of compression codecs.
  • Custom tile size
  • Lossless repackaging / transcoding (to zarr/NGFF or TIFF) from:

    • SVS (JPEG compressed)
    • OME-TIFF (single image, JPEG and JPEG2000 (J2K) compressed)
    • Generic Tiled TIFF (JPEG, JPEG2000, and WebP compressed)
    • DICOM WSI (JPEG and JPEG2000 (J2K) compressed)
Read Container Formats
  • OpenSlide Formats:

    • Aperio SVS (.svs)
    • Hamamatsu (.vms, .vmu, .ndpi)
    • Leica (.scn)
    • Mirax MRXS (.mrxs)
    • Sakura (.svslide)
    • Trestle (.tif)
    • Ventana (.bif, .tif)
    • Generic tiled TIFF (.tif; DEFLATE, JPEG, and Webp
compressed)
  • Other Tiled TIFFs
(tifffile supported
formats)

    • Tiled with various codecs: e.g. JPEG XL, JPEG 2000, WebP, and zstd.
    • RGB/brightfield OME-TIFF.
  • JP2 (via
glymur and
OpenJPEG)

    • Including Omnyx JP2 files.
  • Zarr
    • Single array.
    • Group of (multiresolution) arrays.
    • NGFF v0.4.
  • DICOM WSI (via
wsidicom)

Write Container Formats
  • TIFF

    • Generic Tiled / Pyramid TIFF
    • OME-TIFF
    • SVS
  • JP2
  • Zarr (NGFF v0.4)
  • DICOM (.dcm)
Notes & FAQs
Python on Windows handles multiprocessing
differenly
to POSIX/UNIX-like systems. I suggest using the Windows Subsystem for
Linux on Windows
to ensure that wsic functions correctly and efficiently.
Other Tools
There are many other great tools in this space. Below are some other
tools for converting WSIs.
  1. bfconvert
Part of the Bio-Formats command line tools. Uses bioformats to convert
from many formats to OME-TIFF.
  2. biofromats2raw
Convert from Bio-Formats formats to zarr.
  3. isyntax2raw Convert from Philips' iSyntax format to a zarr using Philips' SDK.
  4. wsidicomiser Convert OpenSlide images to WSI DICOM.
Credits
This package was created with
Cookiecutter and the
audreyr/cookiecutter-pypackage
project template.
About
Whole Slide image (WSI) conversion for brightfield histology images
Resources
Readme
License
Contributing
Contributing
Activity
Custom properties
Stars
1 star
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
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
wsic
Gitmojiimageimage
Python applicationDocumentation Status
imageimageimage
Whole Slide Image (WSI) conversion for brightfield histology images.
Provides a command line interface (CLI) for easy convertion between
formats:
Usage: wsic convert [OPTIONS]
Convert a WSI.
Options:
-i, --in-path PATH Path to WSI to read from.
-o, --out-path PATH The path to output to.
-t, --tile-size <INTEGER INTEGER>...
The size of the tiles to write.
-rt, --read-tile-size <INTEGER INTEGER>...
The size of the tiles to read.
-w, --workers INTEGER The number of workers to use.
-c, --compression [blosc|deflate|jpeg xl|jpeg-ls|jpeg|jpeg2000|lzw|png|webp|zstd]
The compression to use.
-cl, --compression-level INTEGER
The compression level to use.
-d, --downsample INTEGER The downsample factor to use.
-mpp, --microns-per-pixel <FLOAT FLOAT>...
The microns per pixel to use.
-ome, --ome / --no-ome Save with OME-TIFF metadata (OME-TIFF and
NGFF).
--overwrite / --no-overwrite Whether to overwrite the output file.
-to, --timeout FLOAT Timeout in seconds for reading a tile.
-W, --writer [auto|jp2|svs|tiff|zarr]
The writer to use. Overrides writer detected
by output file extension.
-s, --store [dir|ndir|zip|sqlite]
The store to use (zarr/NGFF only). Defaults
to ndir (nested directory).
-h, --help Show this message and exit.

A demonstration of converting a JP2 file to a pyramid TIFF.
Getting Started
For basic usage see the documentation page "How do
I...?".
Features
  • Reading and writing several container formats.
  • Support for a wide range of compression codecs.
  • Custom tile size
  • Lossless repackaging / transcoding (to zarr/NGFF or TIFF) from:

    • SVS (JPEG compressed)
    • OME-TIFF (single image, JPEG and JPEG2000 (J2K) compressed)
    • Generic Tiled TIFF (JPEG, JPEG2000, and WebP compressed)
    • DICOM WSI (JPEG and JPEG2000 (J2K) compressed)
Read Container Formats
  • OpenSlide Formats:

    • Aperio SVS (.svs)
    • Hamamatsu (.vms, .vmu, .ndpi)
    • Leica (.scn)
    • Mirax MRXS (.mrxs)
    • Sakura (.svslide)
    • Trestle (.tif)
    • Ventana (.bif, .tif)
    • Generic tiled TIFF (.tif; DEFLATE, JPEG, and Webp
compressed)
  • Other Tiled TIFFs
(tifffile supported
formats)

    • Tiled with various codecs: e.g. JPEG XL, JPEG 2000, WebP, and zstd.
    • RGB/brightfield OME-TIFF.
  • JP2 (via
glymur and
OpenJPEG)

    • Including Omnyx JP2 files.
  • Zarr
    • Single array.
    • Group of (multiresolution) arrays.
    • NGFF v0.4.
  • DICOM WSI (via
wsidicom)

Write Container Formats
  • TIFF

    • Generic Tiled / Pyramid TIFF
    • OME-TIFF
    • SVS
  • JP2
  • Zarr (NGFF v0.4)
  • DICOM (.dcm)
Notes & FAQs
Python on Windows handles multiprocessing
differenly
to POSIX/UNIX-like systems. I suggest using the Windows Subsystem for
Linux on Windows
to ensure that wsic functions correctly and efficiently.
Other Tools
There are many other great tools in this space. Below are some other
tools for converting WSIs.
  1. bfconvert
Part of the Bio-Formats command line tools. Uses bioformats to convert
from many formats to OME-TIFF.
  2. biofromats2raw
Convert from Bio-Formats formats to zarr.
  3. isyntax2raw Convert from Philips' iSyntax format to a zarr using Philips' SDK.
  4. wsidicomiser Convert OpenSlide images to WSI DICOM.
Credits
This package was created with
Cookiecutter and the
audreyr/cookiecutter-pypackage
project template.
About
Whole Slide image (WSI) conversion for brightfield histology images
Resources
Readme
License
Contributing
Contributing
Activity
Custom properties
Stars
1 star
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
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
wsic
Gitmojiimageimage
Python applicationDocumentation Status
imageimageimage
Whole Slide Image (WSI) conversion for brightfield histology images.
Provides a command line interface (CLI) for easy convertion between
formats:
Usage: wsic convert [OPTIONS]
Convert a WSI.
Options:
-i, --in-path PATH Path to WSI to read from.
-o, --out-path PATH The path to output to.
-t, --tile-size <INTEGER INTEGER>...
The size of the tiles to write.
-rt, --read-tile-size <INTEGER INTEGER>...
The size of the tiles to read.
-w, --workers INTEGER The number of workers to use.
-c, --compression [blosc|deflate|jpeg xl|jpeg-ls|jpeg|jpeg2000|lzw|png|webp|zstd]
The compression to use.
-cl, --compression-level INTEGER
The compression level to use.
-d, --downsample INTEGER The downsample factor to use.
-mpp, --microns-per-pixel <FLOAT FLOAT>...
The microns per pixel to use.
-ome, --ome / --no-ome Save with OME-TIFF metadata (OME-TIFF and
NGFF).
--overwrite / --no-overwrite Whether to overwrite the output file.
-to, --timeout FLOAT Timeout in seconds for reading a tile.
-W, --writer [auto|jp2|svs|tiff|zarr]
The writer to use. Overrides writer detected
by output file extension.
-s, --store [dir|ndir|zip|sqlite]
The store to use (zarr/NGFF only). Defaults
to ndir (nested directory).
-h, --help Show this message and exit.

A demonstration of converting a JP2 file to a pyramid TIFF.
Getting Started
For basic usage see the documentation page "How do
I...?".
Features
  • Reading and writing several container formats.
  • Support for a wide range of compression codecs.
  • Custom tile size
  • Lossless repackaging / transcoding (to zarr/NGFF or TIFF) from:

    • SVS (JPEG compressed)
    • OME-TIFF (single image, JPEG and JPEG2000 (J2K) compressed)
    • Generic Tiled TIFF (JPEG, JPEG2000, and WebP compressed)
    • DICOM WSI (JPEG and JPEG2000 (J2K) compressed)
Read Container Formats
  • OpenSlide Formats:

    • Aperio SVS (.svs)
    • Hamamatsu (.vms, .vmu, .ndpi)
    • Leica (.scn)
    • Mirax MRXS (.mrxs)
    • Sakura (.svslide)
    • Trestle (.tif)
    • Ventana (.bif, .tif)
    • Generic tiled TIFF (.tif; DEFLATE, JPEG, and Webp
compressed)
  • Other Tiled TIFFs
(tifffile supported
formats)

    • Tiled with various codecs: e.g. JPEG XL, JPEG 2000, WebP, and zstd.
    • RGB/brightfield OME-TIFF.
  • JP2 (via
glymur and
OpenJPEG)

    • Including Omnyx JP2 files.
  • Zarr
    • Single array.
    • Group of (multiresolution) arrays.
    • NGFF v0.4.
  • DICOM WSI (via
wsidicom)

Write Container Formats
  • TIFF

    • Generic Tiled / Pyramid TIFF
    • OME-TIFF
    • SVS
  • JP2
  • Zarr (NGFF v0.4)
  • DICOM (.dcm)
Notes & FAQs
Python on Windows handles multiprocessing
differenly
to POSIX/UNIX-like systems. I suggest using the Windows Subsystem for
Linux on Windows
to ensure that wsic functions correctly and efficiently.
Other Tools
There are many other great tools in this space. Below are some other
tools for converting WSIs.
  1. bfconvert
Part of the Bio-Formats command line tools. Uses bioformats to convert
from many formats to OME-TIFF.
  2. biofromats2raw
Convert from Bio-Formats formats to zarr.
  3. isyntax2raw Convert from Philips' iSyntax format to a zarr using Philips' SDK.
  4. wsidicomiser Convert OpenSlide images to WSI DICOM.
Credits
This package was created with
Cookiecutter and the
audreyr/cookiecutter-pypackage
project template.
About
Whole Slide image (WSI) conversion for brightfield histology images
Resources
Readme
License
Contributing
Contributing
Activity
Custom properties
Stars
1 star
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
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
wsic
Gitmojiimageimage
Python applicationDocumentation Status
imageimageimage
Whole Slide Image (WSI) conversion for brightfield histology images.
Provides a command line interface (CLI) for easy convertion between
formats:
Usage: wsic convert [OPTIONS]
Convert a WSI.
Options:
-i, --in-path PATH Path to WSI to read from.
-o, --out-path PATH The path to output to.
-t, --tile-size <INTEGER INTEGER>...
The size of the tiles to write.
-rt, --read-tile-size <INTEGER INTEGER>...
The size of the tiles to read.
-w, --workers INTEGER The number of workers to use.
-c, --compression [blosc|deflate|jpeg xl|jpeg-ls|jpeg|jpeg2000|lzw|png|webp|zstd]
The compression to use.
-cl, --compression-level INTEGER
The compression level to use.
-d, --downsample INTEGER The downsample factor to use.
-mpp, --microns-per-pixel <FLOAT FLOAT>...
The microns per pixel to use.
-ome, --ome / --no-ome Save with OME-TIFF metadata (OME-TIFF and
NGFF).
--overwrite / --no-overwrite Whether to overwrite the output file.
-to, --timeout FLOAT Timeout in seconds for reading a tile.
-W, --writer [auto|jp2|svs|tiff|zarr]
The writer to use. Overrides writer detected
by output file extension.
-s, --store [dir|ndir|zip|sqlite]
The store to use (zarr/NGFF only). Defaults
to ndir (nested directory).
-h, --help Show this message and exit.

A demonstration of converting a JP2 file to a pyramid TIFF.
Getting Started
For basic usage see the documentation page "How do
I...?".
Features
  • Reading and writing several container formats.
  • Support for a wide range of compression codecs.
  • Custom tile size
  • Lossless repackaging / transcoding (to zarr/NGFF or TIFF) from:

    • SVS (JPEG compressed)
    • OME-TIFF (single image, JPEG and JPEG2000 (J2K) compressed)
    • Generic Tiled TIFF (JPEG, JPEG2000, and WebP compressed)
    • DICOM WSI (JPEG and JPEG2000 (J2K) compressed)
Read Container Formats
  • OpenSlide Formats:

    • Aperio SVS (.svs)
    • Hamamatsu (.vms, .vmu, .ndpi)
    • Leica (.scn)
    • Mirax MRXS (.mrxs)
    • Sakura (.svslide)
    • Trestle (.tif)
    • Ventana (.bif, .tif)
    • Generic tiled TIFF (.tif; DEFLATE, JPEG, and Webp
compressed)
  • Other Tiled TIFFs
(tifffile supported
formats)

    • Tiled with various codecs: e.g. JPEG XL, JPEG 2000, WebP, and zstd.
    • RGB/brightfield OME-TIFF.
  • JP2 (via
glymur and
OpenJPEG)

    • Including Omnyx JP2 files.
  • Zarr
    • Single array.
    • Group of (multiresolution) arrays.
    • NGFF v0.4.
  • DICOM WSI (via
wsidicom)

Write Container Formats
  • TIFF

    • Generic Tiled / Pyramid TIFF
    • OME-TIFF
    • SVS
  • JP2
  • Zarr (NGFF v0.4)
  • DICOM (.dcm)
Notes & FAQs
Python on Windows handles multiprocessing
differenly
to POSIX/UNIX-like systems. I suggest using the Windows Subsystem for
Linux on Windows
to ensure that wsic functions correctly and efficiently.
Other Tools
There are many other great tools in this space. Below are some other
tools for converting WSIs.
  1. bfconvert
Part of the Bio-Formats command line tools. Uses bioformats to convert
from many formats to OME-TIFF.
  2. biofromats2raw
Convert from Bio-Formats formats to zarr.
  3. isyntax2raw Convert from Philips' iSyntax format to a zarr using Philips' SDK.
  4. wsidicomiser Convert OpenSlide images to WSI DICOM.
Credits
This package was created with
Cookiecutter and the
audreyr/cookiecutter-pypackage
project template.
About
Whole Slide image (WSI) conversion for brightfield histology images
Resources
Readme
License
Contributing
Contributing
Activity
Custom properties
Stars
1 star
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
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); }
})();
})();

Skip to content
BranchesTags
Repository files navigation
wsic
Gitmojiimageimage
Python applicationDocumentation Status
imageimageimage
Whole Slide Image (WSI) conversion for brightfield histology images.
Provides a command line interface (CLI) for easy convertion between
formats:
Usage: wsic convert [OPTIONS]
Convert a WSI.
Options:
-i, --in-path PATH Path to WSI to read from.
-o, --out-path PATH The path to output to.
-t, --tile-size <INTEGER INTEGER>...
The size of the tiles to write.
-rt, --read-tile-size <INTEGER INTEGER>...
The size of the tiles to read.
-w, --workers INTEGER The number of workers to use.
-c, --compression [blosc|deflate|jpeg xl|jpeg-ls|jpeg|jpeg2000|lzw|png|webp|zstd]
The compression to use.
-cl, --compression-level INTEGER
The compression level to use.
-d, --downsample INTEGER The downsample factor to use.
-mpp, --microns-per-pixel <FLOAT FLOAT>...
The microns per pixel to use.
-ome, --ome / --no-ome Save with OME-TIFF metadata (OME-TIFF and
NGFF).
--overwrite / --no-overwrite Whether to overwrite the output file.
-to, --timeout FLOAT Timeout in seconds for reading a tile.
-W, --writer [auto|jp2|svs|tiff|zarr]
The writer to use. Overrides writer detected
by output file extension.
-s, --store [dir|ndir|zip|sqlite]
The store to use (zarr/NGFF only). Defaults
to ndir (nested directory).
-h, --help Show this message and exit.

A demonstration of converting a JP2 file to a pyramid TIFF.
Getting Started
For basic usage see the documentation page "How do
I...?".
Features
  • Reading and writing several container formats.
  • Support for a wide range of compression codecs.
  • Custom tile size
  • Lossless repackaging / transcoding (to zarr/NGFF or TIFF) from:

    • SVS (JPEG compressed)
    • OME-TIFF (single image, JPEG and JPEG2000 (J2K) compressed)
    • Generic Tiled TIFF (JPEG, JPEG2000, and WebP compressed)
    • DICOM WSI (JPEG and JPEG2000 (J2K) compressed)
Read Container Formats
  • OpenSlide Formats:

    • Aperio SVS (.svs)
    • Hamamatsu (.vms, .vmu, .ndpi)
    • Leica (.scn)
    • Mirax MRXS (.mrxs)
    • Sakura (.svslide)
    • Trestle (.tif)
    • Ventana (.bif, .tif)
    • Generic tiled TIFF (.tif; DEFLATE, JPEG, and Webp
compressed)
  • Other Tiled TIFFs
(tifffile supported
formats)

    • Tiled with various codecs: e.g. JPEG XL, JPEG 2000, WebP, and zstd.
    • RGB/brightfield OME-TIFF.
  • JP2 (via
glymur and
OpenJPEG)

    • Including Omnyx JP2 files.
  • Zarr
    • Single array.
    • Group of (multiresolution) arrays.
    • NGFF v0.4.
  • DICOM WSI (via
wsidicom)

Write Container Formats
  • TIFF

    • Generic Tiled / Pyramid TIFF
    • OME-TIFF
    • SVS
  • JP2
  • Zarr (NGFF v0.4)
  • DICOM (.dcm)
Notes & FAQs
Python on Windows handles multiprocessing
differenly
to POSIX/UNIX-like systems. I suggest using the Windows Subsystem for
Linux on Windows
to ensure that wsic functions correctly and efficiently.
Other Tools
There are many other great tools in this space. Below are some other
tools for converting WSIs.
  1. bfconvert
Part of the Bio-Formats command line tools. Uses bioformats to convert
from many formats to OME-TIFF.
  2. biofromats2raw
Convert from Bio-Formats formats to zarr.
  3. isyntax2raw Convert from Philips' iSyntax format to a zarr using Philips' SDK.
  4. wsidicomiser Convert OpenSlide images to WSI DICOM.
Credits
This package was created with
Cookiecutter and the
audreyr/cookiecutter-pypackage
project template.
About
Whole Slide image (WSI) conversion for brightfield histology images
Resources
Readme
License
Contributing
Contributing
Activity
Custom properties
Stars
1 star
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages