Supported formats
Every image, table and folder format Plexora imports, read from the importer's own lists.
Generated from Plexora 0.0.55
Plexora decides what a file is from its contents first and its extension second, so the tables below list what each extension is tried as. A file that does not match what its extension suggests is still identified correctly or refused with a message saying why.
Images
| Extension | Read as | Notes |
|---|---|---|
.bif | Brightfield whole-slide image | Roche Ventana whole-slide image, read as brightfield. Local or at a web address. |
.czi | Image | Zeiss CZI image (ZEN 2011 on), a slide scan with its own resolution levels or an acquisition with its channels, planes and time points; each scene of a multi-scene file as a sample of its own. Local only. |
.dcm | Image | DICOM whole-slide image (a folder of .dcm files), read with wsidicom; a fluorescence slide's focal planes open as a z-stack. Local or at a web address (pip install "plexora[remote]"). |
.dv | Image | DeltaVision image (softWoRx). Local only. |
.ets | Image | One scan of an Olympus/Evident cellSens VSI, opened without its .vsi (an H&E scan sent on its own opens as brightfield), with the scan's own resolution levels. Channel names and pixel size are in the .vsi, so they are read from it when the file is still in its _name_/stack<n> folder beside the .vsi, and are missing otherwise. Local only. |
.ims | Image | Imaris image (HDF5, or the TIFF-based file Imaris 3 and 4 wrote), with every channel, plane and resolution level and the voxel size the file states, or a label mask, 2-D or 3-D. Local or at a web address. |
.jpeg | Image | Single-plane RGB or grayscale image. Local or at a web address. |
.jpg | Image | Single-plane RGB or grayscale image. Local or at a web address. |
.kfb | Image | KFBio whole-slide scan, with the scan's own resolution levels. Local only. |
.lif | Image | Leica LIF project (LAS AF and LAS X), each image as a sample of its own, with a tile scan placed by its stage positions. Local only. |
.lof | Image | Leica LOF image (LAS X). Local only. |
.lsm | Image | Zeiss LSM confocal image (LSM 510 to 880), with its channels (a lambda stack's by wavelength), planes and time points. Local only. |
.mcd | Image | Hyperion imaging mass cytometry file, each acquisition as a sample of its own, with its panel's channel names. Local only. |
.mrxs | Brightfield whole-slide image | 3DHISTECH whole-slide image. A brightfield slide needs the wsi extra (pip install "plexora[wsi]"); a fluorescence slide opens with its channels named, without it. Local only. |
.nd2 | Image | Nikon ND2 image, every version from the JPEG 2000 files of NIS-Elements 2 on; each position of a multi-point acquisition as a sample of its own. Local only. |
.ndpi | Brightfield whole-slide image | Hamamatsu whole-slide image, read as brightfield. Local or at a web address. |
.ndpis | Image | Hamamatsu NanoZoomer fluorescence scan, one NDPI file per channel listed by the .ndpis. Local only. |
.oib | Image | Olympus FluoView OIB image. Local only. |
.oif | Image | Olympus FluoView OIF image, with its .oif.files folder. Local only. |
.oir | Image | Olympus/Evident FluoView OIR image (FV1200 on). Local only. |
.png | Image | Single-plane RGB or grayscale image. Local or at a web address. |
.qptiff | Image | Akoya PhenoImager (Vectra/Polaris) multiplex image. Local or at a web address. |
.r3d | Image | DeltaVision image (softWoRx). Local only. |
.scn | Brightfield whole-slide image | Leica whole-slide image; a brightfield scan is read as brightfield and a fluorescence scan as its channels. Local or at a web address. |
.svs | Brightfield whole-slide image | Aperio whole-slide image, read as brightfield. Local or at a web address. |
.svslide | Brightfield whole-slide image | Sakura whole-slide image. Needs the wsi extra. Local only. |
.tif | Image | TIFF or OME-TIFF image (a z-stack opens plane by plane), or a label mask, 2-D or 3-D. An image may also be at a web address. |
.tiff | Image | TIFF or OME-TIFF image (a z-stack opens plane by plane), or a label mask, 2-D or 3-D. An image may also be at a web address. |
.vsi | Image | Olympus/Evident cellSens VSI slide scan or acquisition, read from the _name_ folder beside the file, with the scan's own resolution levels; each scanned region as a sample of its own. Local only. |
.xlef | Image | Leica XLEF export (LAS X), with its frames as LOF or TIFF files beside it. Local only. |
.zvi | Image | Zeiss AxioVision ZVI image, with its channels, planes and the channel names and pixel size AxioVision stored. Local only. |
Cell tables
| Extension | Read as | Notes |
|---|---|---|
.csv | Delimited table | Comma- or semicolon-separated cell table. |
.h5ad | AnnData | AnnData. Coordinates from obsm["spatial"] or two obs columns. |
.parquet | Parquet table | Parquet cell table. |
.tsv | Delimited table | Tab-separated cell table (the separator is read from the header line). |
.txt | Delimited table | Tab-, comma- or semicolon-separated cell table. |
Folders and run outputs
| Folder or store | What Plexora reads | Guide |
|---|---|---|
OME-Zarr (.zarr folder) | A multiscale image, local or at an https://, s3://, gs:// or az:// address. | Opening images and datasets |
SpatialData (.zarr folder with tables/) | Images, labels, points and a cell table from one store. | Opening images and datasets |
| DICOM whole-slide folder | A pyramidal brightfield or multiplex slide stored as DICOM instances, local or in a bucket (s3://, gs://, az://). | Opening images and datasets |
Not supported
These formats are recognised by name but not imported. See Opening images and datasets for what to do instead.
| Format | Status |
|---|---|
| NanoString CosMx output | Not supported. Export a cell table and image and import them as files. |
| Vizgen MERSCOPE output | Not supported. Export a cell table and image and import them as files. |
| Feather tables | Not supported. Convert to Parquet or CSV. |
| GeoJSON shapes | Recorded on import but not drawn. |
Data node resources
A data node serves resources of these kinds: image, segmentation, table. See Data nodes.