Supported file formats¶
CloudScope loads commercial microscopy formats and open image formats. The same loaders are available in the desktop app and the browser app.
CloudScope loads files lazily — image pixels and analysis load only when you select a file. This lets you browse folders with many files without loading everything into memory at once.
Supported formats¶
CloudScope supports these commercial microscopy formats:
| Format | Extension | Notes |
|---|---|---|
| Olympus / Evident | .oir |
May include a reference/overview image. Physical units and reference spatial scales are loaded from the file when available. |
| Zeiss | .czi |
May include a reference/overview image and scan path. Physical units are loaded from the file when available. |
| Nikon | .nd2 |
Nikon NIS-Elements acquisitions. |
and these open image formats:
| Format | Extension | Notes |
|---|---|---|
| TIFF | .tif |
Generic TIFF image files, including multi-channel images. |
| OME-Zarr | .ome.zarr |
Directory-backed OME-Zarr stores (load). |
Notes¶
- Physical units. OIR and CZI loaders often populate Y/X physical unit size and labels (and reference-image scales when a reference exists). Plain TIFF files may lack embedded scaling — use GUI: Image header to set or override units, then save.
- Reference images. OIR and CZI files often, but not always, include a reference or overview image and scan-path metadata. See Kymograph reference images. Export a reference with Save Reference As Tif (see Saved file formats).
- Load reporting. Files that cannot be read are reported as warnings (missing file, unsupported type, or read error) rather than failing the whole folder load.
CloudScope's CZI and OIR support builds on file-format work by Christoph Gohlke.
Sample data¶
To try CloudScope without your own files, load the sample datasets from the history menu in the load/save controls:
- Load Velocity Sample Data — OIR kymograph data for velocity analysis
- Load Diameter Sample Data — TIFF kymograph data for diameter analysis
See Using the GUI for screenshots and menu details.