Open microscope files and check reader support¶
VIPP 0.15.0a2 includes native microscope readers in plugin and desktop installations. Use Image Source → Reader support to check this environment or arrange missing-package setup. For older software, use its versioned installation manual.
What is included?¶
| File family | Included reader |
|---|---|
| TIFF, OME-TIFF and Zeiss LSM | TIFF reader and compression codecs |
| Zeiss CZI | Native CZI reader |
| Leica LIF, LOF and XLIF | Native Leica reader |
| Nikon ND2 | ND2 reader, including legacy compression support |
| Olympus OIF, OIB and OIR | Native Olympus readers |
These readers are standard in the napari plugin and Windows/macOS desktop installations. You do not need to choose a microscope extra during installation. Other existing inputs, such as OME-Zarr and ordinary images, remain available.
Bio-Formats remains optional. It provides the IMS/VSI route and broader fallback support. Its current Python package can fetch Java and Bio-Formats when first used, so that first read may require internet access and extra time. Bio-Formats installation details.
Check or fix a reader¶
- Select any Image Source node, including a newly added node. You do not need to open a file or change its source mode.
- Expand the separate Reader support inspector section, marked System information. It is normally collapsed, outside the image parameters.
- Read the status beside the format you need. Reader loads means the dependency/import check passed; it does not validate the selected image.
- If a package is missing, click Install [reader]…. If a reader cannot load, retry its check or open Reader help.
When an image fails to open, relevant reader actions also appear directly in Image Source, without requiring you to find a Settings page. Use Retry opening this image after a temporary problem is resolved.
Reader support describes this installation, not a processing setting for the selected image. The first expansion checks support in the background. Results are cached for the VIPP session, including while switching nodes. Use Recheck reader support to refresh them explicitly; restarting VIPP starts a new cache.
Format names are bold in the normal text colour. The status beside each name is green when the reader loads, yellow when support is missing or needs an update, and red when loading failed. Scroll the inspector to see all formats and recovery actions.
Install missing support¶
- In the separate setup window, confirm that the displayed environment is the VIPP/napari installation you want to fix.
- Click Review packages. This downloads a proposed package set from PyPI; it does not install it yet.
- Review the package list and approve Install after VIPP / napari closes.
- Save your work and close VIPP/napari normally. Close other Python sessions using that environment too; leave the setup window open.
- Wait for the result, then reopen VIPP/napari and retry the image.
Setup only adds missing packages. It does not replace installed scientific packages, change your images, or automatically close your work. You can close setup while it is waiting to cancel. Do not reopen VIPP during installation.
If the reader needs different installed dependencies, or the environment is shared, externally managed or read-only, setup stops. Use the normal VIPP update route or ask the environment owner to repair it. An import check cannot repair a broken native library by itself.
Before quantitative use¶
Check representative facility files: selected series, axes, scale and units, channels, dtype and pixels. Some vendor acquisitions need companion files or are outside a reader's supported variants. Installing another reader does not override VIPP's saved source identity or silently accept different axes.
See input formats and source contracts for the scientific boundaries and loading problems for other causes of a failed import.