Loading Images

Individual Images

The first step in any computational pathology workflow is to load the image from disk. In PathML this can be done in one line:

wsi = HESlide("../data/CMU-1.svs", name = "example")

Datasets of Images

Using “in-house” datasets from the local filesystem is also supported.

Simply initialize a SlideDataset object by passing a list of individual SlideData objects:

from pathlib import Path
from pathml.core import HESlide, SlideDataset

# assuming that all WSIs are in a single directory, all with .svs file extension
data_dir = Path("/path/to/data/")
wsi_paths = list(data_dir.glob("*.svs"))

# create a list of SlideData objects by loading each path
wsi_list = [HESlide(p) for p in wsi_paths]

# initialize a SlideDataset
dataset = SlideDataset(wsi_list)

Supported slide types

All slides are represented as SlideData objects.

We provide several convenience classes for loading common types of slides:

Slide Classes

Slide Class



H&E stained images.


IHC stained images


Generic multidimensional, multichannel, time-series images (e.g. multiplexed immunofluorescence).


Multiplex images from Vectra platform.


Multiplex images from CODEX platform.

It is also possible to load a slide by using the generic SlideData class and specifying explicitly the slide_type and which backend to use (refer to table below):

wsi = SlideData("../data/CMU-1.svs", name = "example", slide_backend = "openslide", slide_type = types.HE)

For more information on specifying slide_type, see full documentation at SlideType

Supported file formats

Whole-slide images can come in a variety of file formats, depending on the type of image and the scanner used. PathML has several backends for loading images, enabling support for a wide variety of data formats. All backends use the same API for interfacing with other parts of PathML. Choose the appropriate backend for the file format:

PathML Backends


Supported file types


.svs, .tif, .tiff, .bif, .ndpi, .vms, .vmu, .scn, .mrxs, .svslide


.dcm, .dicom
Digital Imaging and Communications in Medicine (DICOM)


Supports almost all commonly used file formats, including multiparametric and volumetric TIFF files.
.1sc, .2fl, .acff, .afi, .afm, .aim, .al3d, .ali, .am,
.amiramesh, .apl, .arf, .avi, .bif, .bin, .bip, .bmp,
.c01, .cfg, .ch5, .cif, .cr2, .crw, .cxd, .czi,
.dat, .dat, .db, .dib, .dm2, .dm3, .dm4, .dti, .dv,
.eps, .epsi, .exp, .fdf, .fff, .ffr, .fits, .fli, .frm,
.gel, .grey, .hdr, .hdr, .hdr, .hdr, .hed, .his, .htd,
.htd, .hx, .i2i, .ics, .ids, .im3, .img, .img, .ims,
.inr, .ipl, .ipm, .ipw, .j2k, .jp2, .jpf, .jpk, .jpx,
.klb, .l2d, .labels, .lei, .lif, .liff, .lim, .lms,
.lsm, .map, .mdb, .mnc, .mng, .mod, .mov, .mrc,
.mrcs, .mrw, .msr, .msr, .mtb, .mvd2, .naf, .nd,
.nef, .nhdr, .nii, .nii.gz, .nrrd, .obf, .obsep, .oib,
.oif, .oir, .ome, .ome.btf, .ome.tf2, .ome.tf8, .ome.tif,
.ome.tiff, .ome.xml, .par, .pbm, .pcoraw, .pcx, .pds,
.pgm, .pic, .pict, .png, .pnl, .ppm, .pr3, .ps, .psd,
.qptiff, .r3d, .raw, .rcpnl, .rec, .rec, .scn, .scn, .sdt,
.seq, .sif, .sld, .sld, .sm2, .sm3, .spc, .spe, .spi,
.st, .stk, .stk, .stp, .sxm, .tfr, .tga, .tif, .tiff,
.tnb, .top, .vff, .vsi, .vws, .wat, .wlz, .wpi,
.xdce, .xml, .xqd, .xqf, .xv, .xys, .zfp, .zfr, .zvi