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Categorical column in points element becomes filled with NaNs #1041

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#1010
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Categorical column in points element becomes filled with NaNs#1041
#1010

Description

@LucaMarconato
LucaMarconato
opened on Jan 3, 2026

To reproduce: https://github.com/giovp/spatialdata-sandbox/blob/main/xenium_2.0.0_io/to_zarr.py

The problem is caused by

spatialdata/src/spatialdata/models/models.py

Line 894 in fe5fae7

data[c] =data[c].cat.set_categories(data[c].head(1).cat.categories)
.

Related to #1009 and could share the same fix proposed in #1010.

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try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
Categorical column in points element becomes filled with `NaN`s · Issue #1041 · scverse/spatialdata · GitHub
      Skip to content
      Categorical column in points element becomes filled with NaNs #1041
      Closed
      #1010
      Closed
      Categorical column in points element becomes filled with NaNs#1041
      #1010
      Description
      @LucaMarconato
      LucaMarconato
      opened on Jan 3, 2026
      To reproduce: https://github.com/giovp/spatialdata-sandbox/blob/main/xenium_2.0.0_io/to_zarr.py
      The problem is caused by 
      spatialdata/src/spatialdata/models/models.py
      
Line 894
in
fe5fae7
      data[c] =data[c].cat.set_categories(data[c].head(1).cat.categories) 
      
.
      Related to #1009 and could share the same fix proposed in #1010.
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, 'i');
if (__m === '*' || __re.test(location.href)) {
// Force GitHub README to respect dark mode
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var style = document.createElement('style');
style.textContent = '
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color-scheme: dark light;
}
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(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Categorical column in points element becomes filled with `NaN`s · Issue #1041 · scverse/spatialdata · GitHub
          Skip to content
          Categorical column in points element becomes filled with NaNs #1041
          Closed
          #1010
          Closed
          Categorical column in points element becomes filled with NaNs#1041
          #1010
          Description
          @LucaMarconato
          LucaMarconato
          opened on Jan 3, 2026
          To reproduce: https://github.com/giovp/spatialdata-sandbox/blob/main/xenium_2.0.0_io/to_zarr.py
          The problem is caused by 
          spatialdata/src/spatialdata/models/models.py
          
Line 894
in
fe5fae7
          data[c] =data[c].cat.set_categories(data[c].head(1).cat.categories) 
          
.
          Related to #1009 and could share the same fix proposed in #1010.
          Metadata
          Metadata
          Assignees
          No one assigned
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, 'i');
if (__m === '*' || __re.test(location.href)) {
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var ref = document.referrer;
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observer.observe(document.body, { childList: true, subtree: true });
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}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
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(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Categorical column in points element becomes filled with `NaN`s · Issue #1041 · scverse/spatialdata · GitHub
              Skip to content
              Categorical column in points element becomes filled with NaNs #1041
              Closed
              #1010
              Closed
              Categorical column in points element becomes filled with NaNs#1041
              #1010
              Description
              @LucaMarconato
              LucaMarconato
              opened on Jan 3, 2026
              To reproduce: https://github.com/giovp/spatialdata-sandbox/blob/main/xenium_2.0.0_io/to_zarr.py
              The problem is caused by 
              spatialdata/src/spatialdata/models/models.py
              
Line 894
in
fe5fae7
              data[c] =data[c].cat.set_categories(data[c].head(1).cat.categories) 
              
.
              Related to #1009 and could share the same fix proposed in #1010.
              Metadata
              Metadata
              Assignees
              No one assigned
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                No labels
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                No type
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, 'i');
if (__m === '*' || __re.test(location.href)) {
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var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',
'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',
'ref', 'ref_src', 'source', 'medium', 'campaign'];
function cleanUrl(url) {
try {
var u = new URL(url, window.location.origin);
var changed = false;
trackingParams.forEach(function(p) {
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observer.observe(document.body, { childList: true, subtree: true });
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} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
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(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
Categorical column in points element becomes filled with `NaN`s · Issue #1041 · scverse/spatialdata · GitHub
                  Skip to content
                  Categorical column in points element becomes filled with NaNs #1041
                  Closed
                  #1010
                  Closed
                  Categorical column in points element becomes filled with NaNs#1041
                  #1010
                  Description
                  @LucaMarconato
                  LucaMarconato
                  opened on Jan 3, 2026
                  To reproduce: https://github.com/giovp/spatialdata-sandbox/blob/main/xenium_2.0.0_io/to_zarr.py
                  The problem is caused by 
                  spatialdata/src/spatialdata/models/models.py
                  
Line 894
in
fe5fae7
                  data[c] =data[c].cat.set_categories(data[c].head(1).cat.categories) 
                  
.
                  Related to #1009 and could share the same fix proposed in #1010.
                  Metadata
                  Metadata
                  Assignees
                  No one assigned
                    Labels
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                    No labels
                    Type
                    No type
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                    No projects
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                      No milestone
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                      No branches or pull requests
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, 'i');
if (__m === '*' || __re.test(location.href)) {
// Auto-enable theater mode on YouTube
(function() {
function tryTheater() {
var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]');
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(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Categorical column in points element becomes filled with `NaN`s · Issue #1041 · scverse/spatialdata · GitHub
                      Skip to content
                      Categorical column in points element becomes filled with NaNs #1041
                      Closed
                      #1010
                      Closed
                      Categorical column in points element becomes filled with NaNs#1041
                      #1010
                      Description
                      @LucaMarconato
                      LucaMarconato
                      opened on Jan 3, 2026
                      To reproduce: https://github.com/giovp/spatialdata-sandbox/blob/main/xenium_2.0.0_io/to_zarr.py
                      The problem is caused by 
                      spatialdata/src/spatialdata/models/models.py
                      
Line 894
in
fe5fae7
                      data[c] =data[c].cat.set_categories(data[c].head(1).cat.categories) 
                      
.
                      Related to #1009 and could share the same fix proposed in #1010.
                      Metadata
                      Metadata
                      Assignees
                      No one assigned
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                        No labels
                        No labels
                        Type
                        No type
                        Projects
                        No projects
                          Milestone
                          No milestone
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                          None yet
                          Development
                          No branches or pull requests
                          Issue actions
                          
, 'i');
if (__m === '*' || __re.test(location.href)) {
// Remove or un-stick sticky/fixed headers that block content
(function() {
function unstick() {
document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) {
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el.style.position = 'static';
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var observer = new MutationObserver(unstick);
observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });
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(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Categorical column in points element becomes filled with `NaN`s · Issue #1041 · scverse/spatialdata · GitHub
                          Skip to content
                          Categorical column in points element becomes filled with NaNs #1041
                          Closed
                          #1010
                          Closed
                          Categorical column in points element becomes filled with NaNs#1041
                          #1010
                          Description
                          @LucaMarconato
                          LucaMarconato
                          opened on Jan 3, 2026
                          To reproduce: https://github.com/giovp/spatialdata-sandbox/blob/main/xenium_2.0.0_io/to_zarr.py
                          The problem is caused by 
                          spatialdata/src/spatialdata/models/models.py
                          
Line 894
in
fe5fae7
                          data[c] =data[c].cat.set_categories(data[c].head(1).cat.categories) 
                          
.
                          Related to #1009 and could share the same fix proposed in #1010.
                          Metadata
                          Metadata
                          Assignees
                          No one assigned
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                            No labels
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                            No type
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                            No projects
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                              No milestone
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                              None yet
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                              No branches or pull requests
                              Issue actions
                              
, 'i');
if (__m === '*' || __re.test(location.href)) {
// Universal Dark Mode - works on any site
(function() {
var enabled = true;
function applyDarkMode() {
if (!enabled) return;
// Create style element if it doesn't exist
var style = document.getElementById('universal-dark-mode-style');
if (!style) {
style = document.createElement('style');
style.id = 'universal-dark-mode-style';
document.head.appendChild(style);
}
// Dark mode CSS - inverts colors but preserves images/video
style.textContent = '
/* Invert everything except media */
html {
filter: invert(1) hue-rotate(180deg) !important;
background: #1a1a2e !important;
}
/* Restore images, videos, iframes, canvas */
img, video, iframe, canvas, svg, picture, [style*="background-image"] {
filter: invert(1) hue-rotate(180deg) !important;
}
/* Preserve specific elements that should not be inverted */
.no-dark-mode, .no-dark-mode *,
[data-theme="light"], [data-theme="light"],
.ace_editor, .ace_editor *,
.CodeMirror, .CodeMirror *,
.monaco-editor, .monaco-editor *,
.markdown-body pre, .markdown-body pre *,
.highlight, .highlight *,
pre code, pre code * {
filter: none !important;
}
/* Fix common UI elements */
.modal, .popup, .dropdown-menu, .tooltip, .popover {
filter: invert(1) hue-rotate(180deg) !important;
background: #2d2d44 !important;
border-color: #444 !important;
}
/* Scrollbars */
::-webkit-scrollbar { background: #1a1a2e !important; }
::-webkit-scrollbar-thumb { background: #444 !important; }
::-webkit-scrollbar-thumb:hover { background: #555 !important; }
/* Selection */
::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
';
}
function removeDarkMode() {
var style = document.getElementById('universal-dark-mode-style');
if (style) style.remove();
}
// Toggle with Alt+Shift+D
document.addEventListener('keydown', function(e) {
if (e.altKey && e.shiftKey && e.key === 'D') {
e.preventDefault();
enabled = !enabled;
if (enabled) {
applyDarkMode();
console.log('[Universal Dark Mode] Enabled');
} else {
removeDarkMode();
console.log('[Universal Dark Mode] Disabled');
}
}
});
// Apply on load
applyDarkMode();
// Re-apply on dynamic content
var observer = new MutationObserver(function(mutations) {
if (enabled && !document.getElementById('universal-dark-mode-style')) {
applyDarkMode();
}
});
observer.observe(document.head, { childList: true });
console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');
})();
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();
Categorical column in points element becomes filled with `NaN`s · Issue #1041 · scverse/spatialdata · GitHub
                              Skip to content
                              Categorical column in points element becomes filled with NaNs #1041
                              Closed
                              #1010
                              Closed
                              Categorical column in points element becomes filled with NaNs#1041
                              #1010
                              Description
                              @LucaMarconato
                              LucaMarconato
                              opened on Jan 3, 2026
                              To reproduce: https://github.com/giovp/spatialdata-sandbox/blob/main/xenium_2.0.0_io/to_zarr.py
                              The problem is caused by 
                              spatialdata/src/spatialdata/models/models.py
                              
Line 894
in
fe5fae7
                              data[c] =data[c].cat.set_categories(data[c].head(1).cat.categories) 
                              
.
                              Related to #1009 and could share the same fix proposed in #1010.
                              Metadata
                              Metadata
                              Assignees
                              No one assigned
                                Labels
                                No labels
                                No labels
                                Type
                                No type
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                                No projects
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                                  No milestone
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                                  None yet
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                                  No branches or pull requests
                                  Issue actions