Wrong spatialplot of Affine Transformation · Issue #103 · scverse/spatialdata-plot

With this issue (#101 ) addressed, I run the tutorial Transformations and coordinate systems, https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/transformations.html

totally following the tutorial, when it comes to the affine transformation, it got wrong spatialplot.

theta = math.pi / 6
rotation = Affine(
[
[math.cos(theta), -math.sin(theta), 0],
[math.sin(theta), math.cos(theta), 0],
[0, 0, 1],
],
input_axes=("x", "y"),
output_axes=("x", "y"),
)
set_transformation(sdata.images["raccoon"], rotation, to_coordinate_system="global")
sdata.pl.render_images().pl.render_labels().pl.render_shapes().pl.show()

FYI:

(spatialdata) $ pip list | grep spatialdata
napari-spatialdata 0.2.4
spatialdata 0.0.10
spatialdata-io 0.0.4
spatialdata-plot 0.0.0 ## pip install the version from spatialdata-plot@bugfix/issue100-get_extent-produces-wrong-output-after-spatial-query

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Please reload this page. scverse /spatialdata-plotPublic Notifications You must be signed in to change notification settings Fork 21 Star 85 Code Issues18 Pull requests4 Actions Projects Security and quality0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights Wrong spatialplot of Affine Transformation #103 Copy link Copy link Closed #162 Closed Wrong spatialplot of Affine Transformation#103 #162 Copy link Assignees Labels bugSomething isn't workingSomething isn't workingpriority: high Milestone v0.1.0 release Description jefferyUstc opened on Jun 14, 2023 Issue body actions With this issue (#101 ) addressed, I run the tutorial Transformations and coordinate systems, https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/transformations.html totally following the tutorial, when it comes to the affine transformation, it got wrong spatialplot. theta = math.pi / 6 rotation = Affine( [ [math.cos(theta), -math.sin(theta), 0], [math.sin(theta), math.cos(theta), 0], [0, 0, 1], ], input_axes=("x", "y"), output_axes=("x", "y"), ) set_transformation(sdata.images["raccoon"], rotation, to_coordinate_system="global") sdata.pl.render_images().pl.render_labels().pl.render_shapes().pl.show() FYI: (spatialdata) $ pip list | grep spatialdata napari-spatialdata 0.2.4 spatialdata 0.0.10 spatialdata-io 0.0.4 spatialdata-plot 0.0.0 ## pip install the version from spatialdata-plot@bugfix/issue100-get_extent-produces-wrong-output-after-spatial-query Reactions are currently unavailable Metadata Metadata Assignees timtreis Labels bugSomething isn't workingSomething isn't workingpriority: high Type No type Projects No projects Milestone v0.1.0 releaseNo due date Relationships None yet Development No branches or pull requests Issue actions Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact You can’t perform that action at this time. , '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 contentNavigation Menu Sign inAppearance settings AI CODE CREATIONGitHub CopilotWrite better code with AI GitHub Copilot appDirect agents from issue to merge MCP RegistryIntegrate external tools DEVELOPER WORKFLOWSActionsAutomate any workflow CodespacesInstant dev environments IssuesPlan and track work Code ReviewManage code changes Code QualityEnforce quality at merge APPLICATION SECURITYGitHub Advanced SecurityFind and fix vulnerabilities Code securitySecure your code as you build Secret protectionStop leaks before they start EXPLOREWhy GitHub Documentation Blog Changelog Marketplace View all features BY COMPANY SIZEEnterprises Small and medium teams Startups Nonprofits BY USE CASEApp Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRYHealthcare Financial services Manufacturing Government View all industries View all solutions EXPLORE BY TOPICAI Software Development DevOps Security View all topics EXPLORE BY TYPECustomer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICESDocumentation Customer support Community forum Trust center Partners View all resources COMMUNITYGitHub SponsorsFund open source developers PROGRAMSSecurity Lab Maintainer Community GitHub Stars Archive Program REPOSITORIESTopics Trending Collections ENTERPRISE SOLUTIONSEnterprise platformAI-powered developer platform AVAILABLE ADD-ONSGitHub Advanced SecurityEnterprise-grade security features Copilot for BusinessEnterprise-grade AI features Premium SupportEnterprise-grade 24/7 support Pricing Sign in Sign upAppearance settings You signed in with another tab or window. 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Please reload this page. scverse /spatialdata-plotPublic Notifications You must be signed in to change notification settings Fork 21 Star 85 Code Issues18 Pull requests4 Actions Projects Security and quality0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights Wrong spatialplot of Affine Transformation #103 Copy link Copy link Closed #162 Closed Wrong spatialplot of Affine Transformation#103 #162 Copy link Assignees Labels bugSomething isn't workingSomething isn't workingpriority: high Milestone v0.1.0 release Description jefferyUstc opened on Jun 14, 2023 Issue body actions With this issue (#101 ) addressed, I run the tutorial Transformations and coordinate systems, https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/transformations.html totally following the tutorial, when it comes to the affine transformation, it got wrong spatialplot. theta = math.pi / 6 rotation = Affine( [ [math.cos(theta), -math.sin(theta), 0], [math.sin(theta), math.cos(theta), 0], [0, 0, 1], ], input_axes=("x", "y"), output_axes=("x", "y"), ) set_transformation(sdata.images["raccoon"], rotation, to_coordinate_system="global") sdata.pl.render_images().pl.render_labels().pl.render_shapes().pl.show() FYI: (spatialdata) $ pip list | grep spatialdata napari-spatialdata 0.2.4 spatialdata 0.0.10 spatialdata-io 0.0.4 spatialdata-plot 0.0.0 ## pip install the version from spatialdata-plot@bugfix/issue100-get_extent-produces-wrong-output-after-spatial-query Reactions are currently unavailable Metadata Metadata Assignees timtreis Labels bugSomething isn't workingSomething isn't workingpriority: high Type No type Projects No projects Milestone v0.1.0 releaseNo due date Relationships None yet Development No branches or pull requests Issue actions Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact You can’t perform that action at this time. , '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 contentNavigation Menu Sign inAppearance settings AI CODE CREATIONGitHub CopilotWrite better code with AI GitHub Copilot appDirect agents from issue to merge MCP RegistryIntegrate external tools DEVELOPER WORKFLOWSActionsAutomate any workflow CodespacesInstant dev environments IssuesPlan and track work Code ReviewManage code changes Code QualityEnforce quality at merge APPLICATION SECURITYGitHub Advanced SecurityFind and fix vulnerabilities Code securitySecure your code as you build Secret protectionStop leaks before they start EXPLOREWhy GitHub Documentation Blog Changelog Marketplace View all features BY COMPANY SIZEEnterprises Small and medium teams Startups Nonprofits BY USE CASEApp Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRYHealthcare Financial services Manufacturing Government View all industries View all solutions EXPLORE BY TOPICAI Software Development DevOps Security View all topics EXPLORE BY TYPECustomer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICESDocumentation Customer support Community forum Trust center Partners View all resources COMMUNITYGitHub SponsorsFund open source developers PROGRAMSSecurity Lab Maintainer Community GitHub Stars Archive Program REPOSITORIESTopics Trending Collections ENTERPRISE SOLUTIONSEnterprise platformAI-powered developer platform AVAILABLE ADD-ONSGitHub Advanced SecurityEnterprise-grade security features Copilot for BusinessEnterprise-grade AI features Premium SupportEnterprise-grade 24/7 support Pricing Sign in Sign upAppearance settings You signed in with another tab or window. 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Please reload this page. scverse /spatialdata-plotPublic Notifications You must be signed in to change notification settings Fork 21 Star 85 Code Issues18 Pull requests4 Actions Projects Security and quality0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights Wrong spatialplot of Affine Transformation #103 Copy link Copy link Closed #162 Closed Wrong spatialplot of Affine Transformation#103 #162 Copy link Assignees Labels bugSomething isn't workingSomething isn't workingpriority: high Milestone v0.1.0 release Description jefferyUstc opened on Jun 14, 2023 Issue body actions With this issue (#101 ) addressed, I run the tutorial Transformations and coordinate systems, https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/transformations.html totally following the tutorial, when it comes to the affine transformation, it got wrong spatialplot. theta = math.pi / 6 rotation = Affine( [ [math.cos(theta), -math.sin(theta), 0], [math.sin(theta), math.cos(theta), 0], [0, 0, 1], ], input_axes=("x", "y"), output_axes=("x", "y"), ) set_transformation(sdata.images["raccoon"], rotation, to_coordinate_system="global") sdata.pl.render_images().pl.render_labels().pl.render_shapes().pl.show() FYI: (spatialdata) $ pip list | grep spatialdata napari-spatialdata 0.2.4 spatialdata 0.0.10 spatialdata-io 0.0.4 spatialdata-plot 0.0.0 ## pip install the version from spatialdata-plot@bugfix/issue100-get_extent-produces-wrong-output-after-spatial-query Reactions are currently unavailable Metadata Metadata Assignees timtreis Labels bugSomething isn't workingSomething isn't workingpriority: high Type No type Projects No projects Milestone v0.1.0 releaseNo due date Relationships None yet Development No branches or pull requests Issue actions Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact You can’t perform that action at this time. , '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 contentNavigation Menu Sign inAppearance settings AI CODE CREATIONGitHub CopilotWrite better code with AI GitHub Copilot appDirect agents from issue to merge MCP RegistryIntegrate external tools DEVELOPER WORKFLOWSActionsAutomate any workflow CodespacesInstant dev environments IssuesPlan and track work Code ReviewManage code changes Code QualityEnforce quality at merge APPLICATION SECURITYGitHub Advanced SecurityFind and fix vulnerabilities Code securitySecure your code as you build Secret protectionStop leaks before they start EXPLOREWhy GitHub Documentation Blog Changelog Marketplace View all features BY COMPANY SIZEEnterprises Small and medium teams Startups Nonprofits BY USE CASEApp Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRYHealthcare Financial services Manufacturing Government View all industries View all solutions EXPLORE BY TOPICAI Software Development DevOps Security View all topics EXPLORE BY TYPECustomer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICESDocumentation Customer support Community forum Trust center Partners View all resources COMMUNITYGitHub SponsorsFund open source developers PROGRAMSSecurity Lab Maintainer Community GitHub Stars Archive Program REPOSITORIESTopics Trending Collections ENTERPRISE SOLUTIONSEnterprise platformAI-powered developer platform AVAILABLE ADD-ONSGitHub Advanced SecurityEnterprise-grade security features Copilot for BusinessEnterprise-grade AI features Premium SupportEnterprise-grade 24/7 support Pricing Sign in Sign upAppearance settings You signed in with another tab or window. 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Please reload this page. scverse /spatialdata-plotPublic Notifications You must be signed in to change notification settings Fork 21 Star 85 Code Issues18 Pull requests4 Actions Projects Security and quality0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights Wrong spatialplot of Affine Transformation #103 Copy link Copy link Closed #162 Closed Wrong spatialplot of Affine Transformation#103 #162 Copy link Assignees Labels bugSomething isn't workingSomething isn't workingpriority: high Milestone v0.1.0 release Description jefferyUstc opened on Jun 14, 2023 Issue body actions With this issue (#101 ) addressed, I run the tutorial Transformations and coordinate systems, https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/transformations.html totally following the tutorial, when it comes to the affine transformation, it got wrong spatialplot. theta = math.pi / 6 rotation = Affine( [ [math.cos(theta), -math.sin(theta), 0], [math.sin(theta), math.cos(theta), 0], [0, 0, 1], ], input_axes=("x", "y"), output_axes=("x", "y"), ) set_transformation(sdata.images["raccoon"], rotation, to_coordinate_system="global") sdata.pl.render_images().pl.render_labels().pl.render_shapes().pl.show() FYI: (spatialdata) $ pip list | grep spatialdata napari-spatialdata 0.2.4 spatialdata 0.0.10 spatialdata-io 0.0.4 spatialdata-plot 0.0.0 ## pip install the version from spatialdata-plot@bugfix/issue100-get_extent-produces-wrong-output-after-spatial-query Reactions are currently unavailable Metadata Metadata Assignees timtreis Labels bugSomething isn't workingSomething isn't workingpriority: high Type No type Projects No projects Milestone v0.1.0 releaseNo due date Relationships None yet Development No branches or pull requests Issue actions Footer © 2026 GitHub, Inc. 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Please reload this page. scverse /spatialdata-plotPublic Notifications You must be signed in to change notification settings Fork 21 Star 85 Code Issues18 Pull requests4 Actions Projects Security and quality0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights Wrong spatialplot of Affine Transformation #103 Copy link Copy link Closed #162 Closed Wrong spatialplot of Affine Transformation#103 #162 Copy link Assignees Labels bugSomething isn't workingSomething isn't workingpriority: high Milestone v0.1.0 release Description jefferyUstc opened on Jun 14, 2023 Issue body actions With this issue (#101 ) addressed, I run the tutorial Transformations and coordinate systems, https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/transformations.html totally following the tutorial, when it comes to the affine transformation, it got wrong spatialplot. theta = math.pi / 6 rotation = Affine( [ [math.cos(theta), -math.sin(theta), 0], [math.sin(theta), math.cos(theta), 0], [0, 0, 1], ], input_axes=("x", "y"), output_axes=("x", "y"), ) set_transformation(sdata.images["raccoon"], rotation, to_coordinate_system="global") sdata.pl.render_images().pl.render_labels().pl.render_shapes().pl.show() FYI: (spatialdata) $ pip list | grep spatialdata napari-spatialdata 0.2.4 spatialdata 0.0.10 spatialdata-io 0.0.4 spatialdata-plot 0.0.0 ## pip install the version from spatialdata-plot@bugfix/issue100-get_extent-produces-wrong-output-after-spatial-query Reactions are currently unavailable Metadata Metadata Assignees timtreis Labels bugSomething isn't workingSomething isn't workingpriority: high Type No type Projects No projects Milestone v0.1.0 releaseNo due date Relationships None yet Development No branches or pull requests Issue actions Footer © 2026 GitHub, Inc. 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Please reload this page. scverse /spatialdata-plotPublic Notifications You must be signed in to change notification settings Fork 21 Star 85 Code Issues18 Pull requests4 Actions Projects Security and quality0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights Wrong spatialplot of Affine Transformation #103 Copy link Copy link Closed #162 Closed Wrong spatialplot of Affine Transformation#103 #162 Copy link Assignees Labels bugSomething isn't workingSomething isn't workingpriority: high Milestone v0.1.0 release Description jefferyUstc opened on Jun 14, 2023 Issue body actions With this issue (#101 ) addressed, I run the tutorial Transformations and coordinate systems, https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/transformations.html totally following the tutorial, when it comes to the affine transformation, it got wrong spatialplot. theta = math.pi / 6 rotation = Affine( [ [math.cos(theta), -math.sin(theta), 0], [math.sin(theta), math.cos(theta), 0], [0, 0, 1], ], input_axes=("x", "y"), output_axes=("x", "y"), ) set_transformation(sdata.images["raccoon"], rotation, to_coordinate_system="global") sdata.pl.render_images().pl.render_labels().pl.render_shapes().pl.show() FYI: (spatialdata) $ pip list | grep spatialdata napari-spatialdata 0.2.4 spatialdata 0.0.10 spatialdata-io 0.0.4 spatialdata-plot 0.0.0 ## pip install the version from spatialdata-plot@bugfix/issue100-get_extent-produces-wrong-output-after-spatial-query Reactions are currently unavailable Metadata Metadata Assignees timtreis Labels bugSomething isn't workingSomething isn't workingpriority: high Type No type Projects No projects Milestone v0.1.0 releaseNo due date Relationships None yet Development No branches or pull requests Issue actions Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact You can’t perform that action at this time. , '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 contentNavigation Menu Sign inAppearance settings AI CODE CREATIONGitHub CopilotWrite better code with AI GitHub Copilot appDirect agents from issue to merge MCP RegistryIntegrate external tools DEVELOPER WORKFLOWSActionsAutomate any workflow CodespacesInstant dev environments IssuesPlan and track work Code ReviewManage code changes Code QualityEnforce quality at merge APPLICATION SECURITYGitHub Advanced SecurityFind and fix vulnerabilities Code securitySecure your code as you build Secret protectionStop leaks before they start EXPLOREWhy GitHub Documentation Blog Changelog Marketplace View all features BY COMPANY SIZEEnterprises Small and medium teams Startups Nonprofits BY USE CASEApp Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRYHealthcare Financial services Manufacturing Government View all industries View all solutions EXPLORE BY TOPICAI Software Development DevOps Security View all topics EXPLORE BY TYPECustomer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICESDocumentation Customer support Community forum Trust center Partners View all resources COMMUNITYGitHub SponsorsFund open source developers PROGRAMSSecurity Lab Maintainer Community GitHub Stars Archive Program REPOSITORIESTopics Trending Collections ENTERPRISE SOLUTIONSEnterprise platformAI-powered developer platform AVAILABLE ADD-ONSGitHub Advanced SecurityEnterprise-grade security features Copilot for BusinessEnterprise-grade AI features Premium SupportEnterprise-grade 24/7 support Pricing Sign in Sign upAppearance settings You signed in with another tab or window. 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Please reload this page. scverse /spatialdata-plotPublic Notifications You must be signed in to change notification settings Fork 21 Star 85 Code Issues18 Pull requests4 Actions Projects Security and quality0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights Wrong spatialplot of Affine Transformation #103 Copy link Copy link Closed #162 Closed Wrong spatialplot of Affine Transformation#103 #162 Copy link Assignees Labels bugSomething isn't workingSomething isn't workingpriority: high Milestone v0.1.0 release Description jefferyUstc opened on Jun 14, 2023 Issue body actions With this issue (#101 ) addressed, I run the tutorial Transformations and coordinate systems, https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/transformations.html totally following the tutorial, when it comes to the affine transformation, it got wrong spatialplot. theta = math.pi / 6 rotation = Affine( [ [math.cos(theta), -math.sin(theta), 0], [math.sin(theta), math.cos(theta), 0], [0, 0, 1], ], input_axes=("x", "y"), output_axes=("x", "y"), ) set_transformation(sdata.images["raccoon"], rotation, to_coordinate_system="global") sdata.pl.render_images().pl.render_labels().pl.render_shapes().pl.show() FYI: (spatialdata) $ pip list | grep spatialdata napari-spatialdata 0.2.4 spatialdata 0.0.10 spatialdata-io 0.0.4 spatialdata-plot 0.0.0 ## pip install the version from spatialdata-plot@bugfix/issue100-get_extent-produces-wrong-output-after-spatial-query Reactions are currently unavailable Metadata Metadata Assignees timtreis Labels bugSomething isn't workingSomething isn't workingpriority: high Type No type Projects No projects Milestone v0.1.0 releaseNo due date Relationships None yet Development No branches or pull requests Issue actions Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact You can’t perform that action at this time.