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Local TIFF support #131

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Local TIFF support #131

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fd655f6
feat: enhance image handling and rendering with local TIFF support
chaichontat Mar 12, 2026
6a2e780
feat: enhance imgIntensity and localTiffSource handling for extreme v…
chaichontat Mar 12, 2026
44fdbfc
feat: implement sample disposal on overwrite and enhance TIFF handling
chaichontat Mar 12, 2026
d611bcb
feat: update ImportInstructionsDialog for improved sample handling an…
chaichontat Mar 12, 2026
ebe7805
more robust
chaichontat Mar 14, 2026
f827f00
feat: refactor BYOD handling and improve dynamic imports for TIFF pro…
chaichontat Mar 14, 2026
3942ece
feat: add shouldEstimateCompositeDefaults function and update conditi…
chaichontat Mar 14, 2026
04460d5
feat: enhance TIFF handling by auto-inferring channel names for multi…
chaichontat Mar 14, 2026
8da0b1b
feat: enhance imgControl component with hover detection and auto-coll…
chaichontat Mar 17, 2026
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5 changes: 4 additions & 1 deletion package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand All @@ -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",
Expand All @@ -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",
Expand Down Expand Up @@ -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",
Expand Down
72 changes: 49 additions & 23 deletions pnpm-lock.yaml
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34 changes: 11 additions & 23 deletions src/lib/components/ImportInstructionsDialog.svelte
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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>

Expand All @@ -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>
Expand Down
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