Open H5AD files in your browser
The file Scanpy and CELLxGENE keep single-cell data in. Open one right here and see its cells, genes and annotations, with no Python. Nothing leaves your device.
Or drop it anywhere on this page
What you'll see
Your H5AD opens as its matrix of cells by genes, with the columns that describe them and the embeddings beside it.
- The matrix • Its size, its storage and how full it is
- Observations and variables • Each column's type
- Layers, embeddings and graphs • Their sizes
- Annotations as CSV • Matrices as NumPy arrays
About H5AD
AnnData is how single-cell studies share their data: Scanpy saves it, CELLxGENE and the Human Cell Atlas offer their datasets as .h5ad, and Seurat users convert to it. Each file is one experiment, often tens of thousands of cells.
At its heart is X, a matrix of observations by variables, as a rule cells by genes, mostly sparse since each cell shows only some genes. Beside it, obs describes each cell with columns like its cell type, var each gene, layers keep other versions of the counts, obsm embeddings such as PCA and UMAP, and obsp graphs of neighbors. It's all kept in HDF5.
Filepeek reads it in your browser. The card shows the size of the matrix, how it's stored and how full it is, every obs and var column with its type, and the layers, embeddings and graphs. obs and var save as CSV, and the matrices open as tables or save as NumPy arrays when they fit in 256 MB spread out in full.
AnnData
.h5ad
Format
- MIME type
- application/x-hdf5
- Made by
- The scverse project
Inside the file
- Holds
- A matrix of cells by genes
- Beside it
- Cell and gene annotations
- Also
- Layers, embeddings, graphs
- Kept in
- HDF5
Opens in every browser
Browsers download H5AD files, and reading one takes Python. Filepeek opens them in Chrome, Edge, Firefox and Safari.
- YouChromeOpens through Filepeek
- YouEdgeOpens through Filepeek
- YouFirefoxOpens through Filepeek
- YouSafariOpens through Filepeek
Apps that open H5AD
- WindowsPython with Scanpy or anndata
- MacPython with Scanpy or anndata
- iPhone and iPadNo app opens it
- AndroidNo app opens it
Questions
How do I open an .h5ad file without Python?
Drop it on this page or choose Peek an H5AD. The matrix, the cells' and genes' columns and the embeddings show at once, with nothing to install.
Can I get the cell annotations as a spreadsheet?
Yes. obs.csv in Arrays holds a row for each cell with every annotation, categories written out. Open it as a table, or save it and open it in Excel. var.csv does the same for genes.
Why won't X open as a table?
Spread out in full, it's bigger than 256 MB, which a table holds here. 50,000 cells by 30,000 genes would take 6 GB. The card still shows its size, storage and how full it is.
My Scanpy won't read a file from a newer version. Can Filepeek?
Often, yes. Newer versions of anndata write encodings older ones don't know, like nullable strings, and Filepeek reads them. The card's File section names the version that wrote it.
What are obs and var?
obs holds a row for each observation, usually a cell, with columns like its cell type and counts. var holds a row for each variable, usually a gene, with columns like its ID. X's rows follow obs and its columns follow var.