> For the complete documentation index, see [llms.txt](https://docs.quilt.bio/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.quilt.bio/quilt-platform-catalog-user/preview.md). # Document Previews The Quilt catalog renders previews of the following file types. Whenever possible, Quilt streams the smallest possible subset of the data needed to generate the preview. Previews are supported for uncompressed files as well as for gzip archives (.gz). ### Plain text previews Quilt can display any plaintext file format, including the following. * Most programming languages, with syntax highlighting (.cpp, .json, .js, .py, .sh, .sql, etc.) * Biological file formats (.bed, .cef, .gff, .fasta, .fastq, .sam, .pdbqt, .vcf, etc.) * Text files (.csv, .md, .readme, .tsv, .txt, etc.) #### Markdown rendering > Changed in Quilt Platform version 1.70 Markdown file previews (.md) render using standard [GitHub-Flavored Markdown](https://github.github.com/gfm/) (GFM), a superset of [CommonMark](https://commonmark.org/). Idiosyncratic Pandoc/PHP-Markdown-Extra shortcuts are no longer supported; author Markdown against the CommonMark + GFM spec for consistent rendering. ### Chemical structures The Quilt catalog uses the [NGL Viewer library](https://github.com/nglviewer/ngl) to render structures. By default, v3000 Molfiles are converted to v2000 by the JavaScript client for rendering. The following file formats are supported: * Mol files (.mol, .mol2, .sdf) * .cif * .ent * .pdb ### Image previews The Quilt Catalog uses a [Lambda function](https://github.com/quiltdata/quilt/tree/master/lambdas/thumbnail) to automatically generate thumbnail previews of common image formats and select microscopy image formats such as .bmp, .gif, .jpg, .jpeg, .png, .webp, .tif, .tiff (including `OME-TIFF`), and .czi. 8-bit, 16-bit, 32/64-bit integer (signed or unsigned), and floating-point pixel data are all supported. Quilt reduces multi-dimensional microscopy images to a single 2D preview: channels are laid out as a grid of per-channel previews, Z-stacks are flattened with a maximum-intensity projection, and time-series show their middle timepoint. #### Display normalization > Thumbnails are a visual aid, not a faithful reproduction of the original pixel values. Previews of high-bit-depth and microscopy images are **contrast-stretched per image** to keep faint, low-contrast detail visible: each grayscale image — and each channel of a multi-channel image — is rescaled from its own range of pixel values, after clipping the most extreme values so a few hot or dead pixels don't flatten the rest. Color previews are stretched the same way, jointly across their channels so the colors aren't skewed. As a result, displayed brightness does **not** represent absolute pixel intensity: it is not comparable between thumbnails, nor between the channels of a multi-channel montage. Ordinary 8-bit images (such as .jpg files) are already display-ready and are shown unchanged. #### Limitations * Very large images may fail to preview if they exceed memory or pixel limits. ### Binary and special file format previews * AnnData (.h5ad) — annotated matrix metadata, with QC metrics for small files * FCS Flow Cytometry files (.fcs) * Media (.mp4, .webm, .flac, .m2t, .mp3, .mp4, .ogg, .ts, .tsa, .tsv, .wav) * Jupyter notebooks (.ipynb) * .parquet * PDF (.pdf) * PowerPoint (.pptx) * Excel (.xls, .xlsx) ### Advanced: HTML rendering and Quilt Package File Server The Quilt Catalog supports HTML and JavaScript in preview via iframes. By default, preview iframes do not have IAM permissions and are therefore unable to access private files in S3. If you wish for your HTML to access data within the enclosing package or bucket (at the viewer's level of permissions) and/or use origin-aware Web APIs such as data storage/cookies, you must opt in to `Enable permissive HTML rendering` in [Bucket settings](/quilt-platform-administrator/admin.md#buckets). This explicitly allows cross-origin resource sharing (CORS). > You should *only enable this feature for buckets where you implicitly trust* the contents of the HTML files. Depending on the context where the HTML file is rendered (package vs bucket view), the iframe gets the following origin: * Inside a package view with permissive rendering **enabled**: the origin is the **Quilt Package File Server**. * Inside a bucket view with permissive rendering **enabled**: the origin is the AWS S3 bucket endpoint. * With permissive rendering **disabled** (irrespective of package or bucket view): the resource is treated as being from a special origin that always fails the same-origin policy ([`allow-same-origin` iframe sandbox token](https://developer.mozilla.org/en-US/docs/Web/HTML/Element/iframe#sandbox) is not set). > An important implication of same-origin policy is that the scripts executed under the same origin share LocalStorage data and cookies. #### Allowing Forms and Popups > New in Quilt Platform version 1.59.0 or higher Enabling Permissive HTML now allows forms and popups to work from iframes. #### Package view example with permissive rendering enabled 1. `report.html` is a file in a package that includes a publicly available JS library and a custom embedded script. 2. Opening `report.html` in a package view generates a new session `temporary-session-id`. 3. The file is served by the **Quilt Package File Server** under the `/temporary-session-id/report.html` path. 4. All relative media and scripts are rendered in the same iframe relative-path format: * `./img.jpg` is resolved to `/temporary-session-id/img.jpg` * `script.js` is resolved to `/temporary-session-id/script.js` 5. The `allow-same-origin` iframe sandbox token is enabled, the origin is the **Quilt Package File Server**, the LocalStorage API is **available**. #### Bucket view example with permissive rendering enabled 1. `report.html` is a file in a bucket `example-bucket` that includes a publicly available JS library and custom embedded script. 2. When opening `report.html` in bucket view, it is served directly by S3 via a signed HTTPS URL, e.g. `https://example-bucket.s3.region.amazonaws.com/report.html?versionId=...&X-Amz-...`. 3. All relative media and scripts are rendered in the same iframe relative-path format: * `./img.jpg` is resolved to `/img.jpg` * `script.js` is resolved to `/script.js` 4. The `allow-same-origin` iframe sandbox token is **enabled**, the origin is the **S3 bucket endpoint** (e.g. `https://example-bucket.s3.region.amazonaws.com`), the LocalStorage API is **available**. #### Example with permissive rendering disabled 1. `report.html` is a file in a bucket `example-bucket` that includes a publicly available JS library and custom embedded script. 2. When opening `report.html` in any view it is served directly by S3 via a signed HTTPS URL, e.g. `https://example-bucket.s3.region.amazonaws.com/report.html?versionId=...&X-Amz-...`. 3. All relative media and scripts are rendered in the same iframe relative-path format: * `./img.jpg` is resolved to `/img.jpg` * `script.js` is resolved to `/script.js` 4. The `allow-same-origin` iframe sandbox token is **disabled**, a virtual unique origin is used (always failing the same-origin policy), the LocalStorage API is **unavailable**. #### Live packages * [Dynamic visualizations; interactive IGV dashboard; Perspective datagrids with images](https://open.quiltdata.com/b/quilt-example/packages/examples/package-file-server) --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://docs.quilt.bio/quilt-platform-catalog-user/preview.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.