Supported File Formats
Biom supports over 30 file formats across scientific imaging, medical imaging, electrophysiology, video, tabular data, and standard images.
No server-side rendering required. Unlike most web-based viewers, Biom decodes and renders scientific images entirely in the browser using WebAssembly. TIFF, CZI, ND2, LIF, and most other microscopy formats open directly — no BioFormats server, no conversion step, no waiting. This covers 95%+ of scientific image file types.
| Format | Extensions | Viewer | Notes |
|---|
| OME-TIFF | .ome.tif, .ome.tiff, .tif, .tiff | Viv/deck.gl | Multi-channel, Z-stacks, time-series. Tile-based streaming for large files. OME-XML metadata. |
| OME-Zarr | .zarr | Viv/deck.gl | Cloud-optimized chunked arrays. Served via presigned URLs or proxy. |
| CZI | .czi | Viv/deck.gl | Zeiss microscopy format. Decoded client-side via WebAssembly. |
| ND2 | .nd2 | Viv/deck.gl | Nikon microscopy format. Decoded client-side via WebAssembly. |
| LIF | .lif | Viv/deck.gl | Leica microscopy format. Decoded client-side via WebAssembly. |
| DICOM | .dcm, .dicom | DICOM Viewer | Medical imaging with window/level presets and series management. |
| FITS | .fits, .fit | Image Viewer | Astronomical images. Input for SExtractor model. |
| Format | Extensions | Viewer | Notes |
|---|
| NWB | .nwb | Spike Viewer | Neurodata Without Borders. HTTP range streaming, 6-hour signed URL TTL. |
| HDF5 | .h5, .hdf5 | Data Viewer | Hierarchical data. Suite2p and SpikeInterface input. |
| SBX | .sbx | — | Scanbox calcium imaging format. Suite2p input. |
| MDA | .mda | — | MountainSort format. SpikeInterface input. |
| BIN/DAT/RAW | .bin, .dat, .raw | — | Raw electrophysiology recordings. SpikeInterface input. |
| NPY/NPZ | .npy, .npz | — | NumPy arrays. Common model output format. |
| MAT | .mat | — | MATLAB data files. |
| Format | Extensions | Viewer | Notes |
|---|
| PNG | .png | Fabric.js Canvas | Standard raster image. |
| JPEG | .jpg, .jpeg | Fabric.js Canvas | Standard raster image. |
| GIF | .gif | Fabric.js Canvas | Animated GIF support. |
| BMP | .bmp | Fabric.js Canvas | Bitmap image. |
| WebP | .webp | Fabric.js Canvas | Modern web image format. |
| SVG | .svg | Fabric.js Canvas | Vector graphics. |
| Format | Extensions | Viewer | Notes |
|---|
| MP4 | .mp4 | Video Player | Frame-by-frame navigation. DeepLabCut and SAM3 input. |
| AVI | .avi | Video Player | Frame-by-frame navigation. |
| MOV | .mov | Video Player | QuickTime format. |
| MKV | .mkv | Video Player | Matroska container. |
| WebM | .webm | Video Player | Web video format. |
| Format | Extensions | Notes |
|---|
| CSV | .csv | Tabular data. Model output, keypoint tracks. |
| TSV | .tsv | Tab-separated values. |
| JSON | .json | Structured data. Pipeline definitions, model configs. |
| PKL | .pkl | Python pickle files. |
| Zarr | .zarr | Chunked array storage. SpikeInterface input/output. |
| Format | Type | Notes |
|---|
| Neuroglancer Precomputed | URL-based | 3D brain volumes and connectomics. Rendered via Neuroglancer viewer. |
| Allen CCFv3 | URL-based | Reference atlas volumes (10um resolution). |
Automatic file routing
Biom automatically routes files to the correct viewer based on type:
- TIFF/OME-TIFF files → Viv/deck.gl scientific viewer (multi-channel, Z-stack support)
- Files > 2 GB → Always routed to Viv viewer regardless of format
- Standard images (PNG, JPEG, etc.) → Fabric.js canvas
- Video files → Video player with frame navigation
- DICOM → DICOM viewer with window/level controls
- NWB → Spike viewer with trace visualization
- Neuroglancer URLs → Neuroglancer 3D viewer
Upload limits
| Method | Max Size | Notes |
|---|
| Simple upload | 100 MB | Single-part upload to Biom Drive |
| Multipart upload | 50 GB | Chunked upload with pause/resume |
| Asset upload | 5 GB | Direct asset upload |
| S3 direct upload | 2 GB | Presigned URL upload |
