Local TIFF support

loopy/feature.py

@@ -2,6 +2,7 @@
 from typing import Callable, Literal, cast
 
 import pandas as pd
+from pandas.api.types import is_object_dtype, is_string_dtype
 from pydantic import validator
 from scipy.sparse import csc_matrix, csr_matrix
 from typing_extensions import Self
@@ -112,15 +113,19 @@ def join_idx(template: pd.DataFrame, feat: pd.DataFrame) -> pd.DataFrame:
     """
 
     for df in [template, feat]:
-        if not df.index.dtype == "object":
+        index = df.index
+        has_string_index = is_string_dtype(index.dtype) or (
+            is_object_dtype(index.dtype) and index.map(lambda value: isinstance(value, str)).all()
+        )
+        if not has_string_index:
             raise ValueError(
                 """Index must be string. This is to prevent subtle bugs.
                 Use`df.index = df.index.astype(str)` and verify that the index is unique with `df.index.is_unique`."""
             )
 
-        if not df.index.is_unique:
+        if not index.is_unique:
             raise ValueError(
-                f"Template (coords) index is not unique. {df.index[df.index.duplicated()]} duplicated"
+                f"Template (coords) index is not unique. {index[index.duplicated()]} duplicated"
             )
 
     joined = template.join(feat, validate="one_to_one")

loopy/sample.py

@@ -6,6 +6,7 @@
 
 import numpy as np
 import pandas as pd
+from pandas.api.types import is_object_dtype, is_string_dtype
 from pydantic import BaseModel
 from typing_extensions import Self
 
@@ -204,7 +205,10 @@ def run():
                 raise ValueError("x and y must be in columns")
             if (df.x.isnull() | df.y.isnull()).any():
                 raise ValueError("x and y must not be null")
-            if df.index.dtype != "object":
+            has_string_index = is_string_dtype(df.index.dtype) or (
+                is_object_dtype(df.index.dtype) and df.index.map(lambda value: isinstance(value, str)).all()
+            )
+            if not has_string_index:
                 raise ValueError(
                     """Index must be string. This is to prevent subtle bugs.
                     Use `df.index = df.index.astype(str)` and verify that it's what you want."""

package.json

@@ -18,7 +18,6 @@
   "devDependencies": {
     "@eslint/js": "^9.35.0",
     "@playwright/test": "1.58.2",
-    "playwright": "1.58.2",
     "@sveltejs/adapter-static": "^3.0.10",
     "@sveltejs/kit": "^2.54.0",
     "@sveltejs/vite-plugin-svelte": "^6.2.4",
@@ -36,6 +35,7 @@
     "@types/wicg-file-system-access": "^2023.10.7",
     "@typescript-eslint/parser": "^8.57.0",
     "@vitest/browser": "^4.1.0",
+    "@vitest/browser-playwright": "4.1.0",
     "autoprefixer": "^10.4.27",
     "clsx": "^2.1.1",
     "d3": "^7.9.0",
@@ -48,6 +48,7 @@
     "globals": "^16.3.0",
     "jsdom": "^28.1.0",
     "node-fetch": "^3.3.2",
+    "playwright": "1.58.2",
     "postcss": "^8.5.8",
     "postcss-load-config": "^6.0.1",
     "prettier": "^3.8.1",
@@ -81,8 +82,10 @@
     "file-saver": "^2.0.5",
     "fzf": "^0.5.2",
     "gdal3.js": "2.8.1",
+    "geotiff": "3.0.5",
     "highlight.js": "^11.11.1",
     "html-to-image": "^1.11.13",
+    "jpegxr": "0.3.0",
     "loam": "^1.2.0",
     "lodash-es": "^4.17.23",
     "lru-cache": "^10.2.2",

src/lib/components/ImportInstructionsDialog.svelte

@@ -9,12 +9,6 @@
 
   const dispatch = createEventDispatcher<{ close: void }>();
 
-  const cliSnippet = `conda activate loopy
-loopy image path/to/image.tif --scale 0.5e-6 --channels DAPI,GFAP
-
-# Optional: integrate spaceranger output
-loopy spaceranger /path/to/spaceranger --out ./loopy --name sample_name`;
-
   const apiSnippet = `from pathlib import Path
 from loopy.sample import Sample
 import pandas as pd
@@ -59,8 +53,8 @@ coords = pd.read_csv("coords.csv", index_col=0)
                   Process Data for Samui
                 </Dialog.Title>
                 <Dialog.Description class="mt-1 text-sm text-neutral-300">
-                  Follow these steps to prepare a sample folder that imports cleanly into the
-                  browser.
+                  Prepare a full sample folder for overlays and metadata, or drag a TIFF directly
+                  into the browser for image-only viewing.
                 </Dialog.Description>
               </div>
               <Dialog.Close
@@ -97,22 +91,11 @@ coords = pd.read_csv("coords.csv", index_col=0)
                     <p class="mt-0.5 text-neutral-300">
                       Choose either the command line or Python API workflow; both populate
                       <code class="font-mono text-neutral-100">sample.json</code>
-                      , which is the data manifest along with actual data files. In this example, we
-                      process a large TIFF image for Samui and overlay it with a point cloud feature.
+                      , which is the data manifest along with actual data files. In this example, we process
+                      a large TIFF image for Samui and overlay it with a point cloud feature.
                     </p>
 
-                    <div class="mt-3 grid gap-4 md:grid-cols-1 -ml-4">
-                      <!-- <div class="rounded-xl border border-neutral-800 bg-neutral-950/70 p-4">
-                  <p class="mb-1 text-xs uppercase tracking-wide text-neutral-400">CLI workflow</p>
-                  <CodeHighlight
-                    code={cliSnippet}
-                    language="bash"
-                    wrap
-                    className="text-xs"
-                    showCopy
-                    ariaLabel="Loopy CLI example"
-                  />
-                </div> -->
+                    <div class="mt-3 -ml-4 grid gap-4 md:grid-cols-1">
                       <div class="rounded-xl border border-neutral-800 bg-neutral-950/70 p-4">
                         <p class="mb-1 text-xs uppercase tracking-wide text-neutral-400">
                           Python API workflow
@@ -159,6 +142,11 @@ coords = pd.read_csv("coords.csv", index_col=0)
                     .
                   </li>
                   <li>Choose your prepared sample folder when prompted.</li>
+                  <li>
+                    Or drag a <code class="font-mono text-neutral-100">.tif</code>
+                    directly onto the page for image-only browsing. Raw TIFF imports are capped at 1 GB
+                    and do not create overlays.
+                  </li>
                 </ol>
               </section>
 
@@ -181,7 +169,7 @@ coords = pd.read_csv("coords.csv", index_col=0)
                   </li>
                   <li>
                     <strong>“Unsupported file type”</strong>
-                    : single-file imports accept ROI/annotation JSON and feature CSVs only.
+                    : single-file imports accept TIFF, ROI/annotation JSON, and feature CSVs only.
                   </li>
                   <li>
                     <strong>Slow conversion/large file size</strong>