File size: 5,354 Bytes
12d2e9e |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 |
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:
.. code-block::
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 :class:`~pathml.core.slide_dataset.SlideDataset` object by passing a list of
individual :class:`~pathml.core.slide_dataset.SlideData` objects:
.. code-block::
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 :class:`~pathml.core.SlideData` objects.
We provide several convenience classes for loading common types of slides:
.. list-table:: Slide Classes
:widths: 20 60
:header-rows: 1
* - Slide Class
- Description
* - :class:`~pathml.core.HESlide`
- H&E stained images.
* - :class:`~pathml.core.IHCSlide`
- IHC stained images
* - :class:`~pathml.core.MultiparametricSlide`
- Generic multidimensional, multichannel, time-series images (e.g. multiplexed immunofluorescence).
* - :class:`~pathml.core.VectraSlide`
- Multiplex images from Vectra platform.
* - :class:`~pathml.core.CODEXSlide`
- Multiplex images from CODEX platform.
It is also possible to load a slide by using the generic :class:`~pathml.core.slide_data.SlideData` class and specifying
explicitly the slide_type and which backend to use (refer to table below):
.. code-block::
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 :class:`~pathml.core.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:
.. list-table:: PathML Backends
:widths: 20 60
:header-rows: 1
* - Backend
- Supported file types
* - :class:`~pathml.core.slide_backends.OpenSlideBackend`
- | ``.svs``, ``.tif``, ``.tiff``, ``.bif``, ``.ndpi``, ``.vms``, ``.vmu``, ``.scn``, ``.mrxs``, ``.svslide``
| `Complete list of file types supported by OpenSlide <https://openslide.org/formats/>`_
* - :class:`~pathml.core.slide_backends.DICOMBackend`
- | ``.dcm``, ``.dicom``
| Digital Imaging and Communications in Medicine (DICOM)
* - :class:`~pathml.core.slide_backends.BioFormatsBackend`
- | 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``
| `Complete list of file types supported by Bio-Formats <https://docs.openmicroscopy.org/bio-formats/latest/supported-formats.html>`_
|