H5AD matrix to CSV
Export a selected AnnData expression matrix as dense CSV, expanding sparse CSR or CSC storage locally.
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Multiple files welcome · processed one at a time
Select a tool to see its supported formats and conversion limits. Large files may exceed your browser’s memory.
Before processing large files
On phones and tablets, start with files under 20 MiB and keep this tab in the foreground. Video, OCR and 3D operations can use several times the input size in memory. Desktop browsers generally have more room, but the 128 MiB job limit is not a guarantee that every file will fit. Smaller batches reduce memory pressure.
Supported input formats
- AnnData annotated HDF5 matrix (.h5ad)
Output format
Comma-separated values (.csv)
Support applies to this conversion direction. Check the limits below for features that may change or be discarded.
Compare all supported formats and conversion limits →How to use H5AD matrix to CSV
- Add your supported file using the chooser or drop zone.
- Review the settings and conversion limits before processing.
- Select Convert files, then download the result.
What to expect
- Modern AnnData HDF5 encodings only. Maximum 64 MiB and 2 million values per dataset. Numeric matrices must be finite and exactly representable; external links and unsupported encodings are rejected.
- Matrix JSON retains sparse indices and pointers; matrix CSV expands to dense values with a 2 million cell cap and no row/column labels. Export obs and var separately for labels. Annotation CSV turns missing values into empty cells. This does not recreate a complete H5AD file.
Engine: h5wasm. The engine may need a first-use download. Your file stays in this browser session.Check conversion engines and offline requirements.
Conversion settings
These settings are available in the converter above.
- Matrix path (for example /X or /layers/counts)
- Default: /X.
About this conversion
Is h5ad matrix to csv free?
Yes. This tool runs on your device without an account or a conversion fee.
Are files uploaded during conversion?
File processing happens locally in your browser. Engines may download their code on first use; your input files are not sent to a conversion server. Read how file privacy works.
What if conversion fails?
Check that the file matches a supported input, review the engine’s limitations and try a smaller representative file. If the engine cannot load, check its engine assets and browser requirements. The app reports failures without switching to a remote converter.
Continue with your output
These tools accept this tool’s output format. Each step has its own settings and fidelity limits.
- Numeric data to HDF5
Create a single selected HDF5 dataset from a numeric matrix or an exported JSON envelope.
- Numeric CSV to Matrix Market
Turn a headerless numeric CSV matrix into sparse Matrix Market coordinate data, omitting zero entries.
- CSV to JSON
Convert CSV locally with an explicit structured-data mapping.
- CSV to TSV
Convert CSV locally with an explicit structured-data mapping.
- CSV to YAML
Convert CSV locally with an explicit structured-data mapping.
- CSV to XML
Convert CSV locally with an explicit structured-data mapping.
More scientific tools
- Inspect AnnData H5AD
Inspect AnnData groups and datasets, including expression matrices, cell observations and gene variables.
- H5AD matrix to JSON
Export an AnnData matrix as JSON, preserving dense values or sparse CSR and CSC indices and pointers.
- H5AD cell annotations to CSV
Export AnnData cell observations to CSV, decoding categorical annotations and preserving cell index labels.
- H5AD gene annotations to CSV
Export AnnData gene variables to CSV, decoding categorical annotations and preserving gene index labels.
- HDF5 dataset to JSON
Select one numeric HDF5 dataset and export its values locally.
- HDF5 dataset to CSV
Select one numeric HDF5 dataset and export its values locally.