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Loading Images |
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Individual Images |
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The first step in any computational pathology workflow is to load the image from disk. |
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In ``PathML`` this can be done in one line: |
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.. code-block:: |
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wsi = HESlide("../data/CMU-1.svs", name = "example") |
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Datasets of Images |
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Using "in-house" datasets from the local filesystem is also supported. |
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Simply initialize a :class:`~pathml.core.slide_dataset.SlideDataset` object by passing a list of |
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individual :class:`~pathml.core.slide_dataset.SlideData` objects: |
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.. code-block:: |
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from pathlib import Path |
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from pathml.core import HESlide, SlideDataset |
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data_dir = Path("/path/to/data/") |
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wsi_paths = list(data_dir.glob("*.svs")) |
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wsi_list = [HESlide(p) for p in wsi_paths] |
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dataset = SlideDataset(wsi_list) |
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Supported slide types |
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--------------------- |
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All slides are represented as :class:`~pathml.core.SlideData` objects. |
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We provide several convenience classes for loading common types of slides: |
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.. list-table:: Slide Classes |
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:widths: 20 60 |
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:header-rows: 1 |
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* - Slide Class |
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- Description |
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* - :class:`~pathml.core.HESlide` |
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- H&E stained images. |
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* - :class:`~pathml.core.IHCSlide` |
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- IHC stained images |
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* - :class:`~pathml.core.MultiparametricSlide` |
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- Generic multidimensional, multichannel, time-series images (e.g. multiplexed immunofluorescence). |
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* - :class:`~pathml.core.VectraSlide` |
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- Multiplex images from Vectra platform. |
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* - :class:`~pathml.core.CODEXSlide` |
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- Multiplex images from CODEX platform. |
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It is also possible to load a slide by using the generic :class:`~pathml.core.slide_data.SlideData` class and specifying |
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explicitly the slide_type and which backend to use (refer to table below): |
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.. code-block:: |
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wsi = SlideData("../data/CMU-1.svs", name = "example", slide_backend = "openslide", slide_type = types.HE) |
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For more information on specifying ``slide_type``, see full documentation at :class:`~pathml.core.SlideType` |
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Supported file formats |
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---------------------- |
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Whole-slide images can come in a variety of file formats, depending on the type of image and the scanner used. |
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``PathML`` has several backends for loading images, enabling support for a wide variety of data formats. |
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All backends use the same API for interfacing with other parts of ``PathML``. Choose the appropriate backend |
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for the file format: |
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.. list-table:: PathML Backends |
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:widths: 20 60 |
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:header-rows: 1 |
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* - Backend |
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- Supported file types |
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* - :class:`~pathml.core.slide_backends.OpenSlideBackend` |
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- | ``.svs``, ``.tif``, ``.tiff``, ``.bif``, ``.ndpi``, ``.vms``, ``.vmu``, ``.scn``, ``.mrxs``, ``.svslide`` |
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| `Complete list of file types supported by OpenSlide <https://openslide.org/formats/>`_ |
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* - :class:`~pathml.core.slide_backends.DICOMBackend` |
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- | ``.dcm``, ``.dicom`` |
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| Digital Imaging and Communications in Medicine (DICOM) |
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* - :class:`~pathml.core.slide_backends.BioFormatsBackend` |
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- | Supports almost all commonly used file formats, including multiparametric and volumetric TIFF files. |
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| ``.1sc``, ``.2fl``, ``.acff``, ``.afi``, ``.afm``, ``.aim``, ``.al3d``, ``.ali``, ``.am``, |
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| ``.amiramesh``, ``.apl``, ``.arf``, ``.avi``, ``.bif``, ``.bin``, ``.bip``, ``.bmp``, |
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| ``.c01``, ``.cfg``, ``.ch5``, ``.cif``, ``.cr2``, ``.crw``, ``.cxd``, ``.czi``, |
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| ``.dat``, ``.dat``, ``.db``, ``.dib``, ``.dm2``, ``.dm3``, ``.dm4``, ``.dti``, ``.dv``, |
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| ``.eps``, ``.epsi``, ``.exp``, ``.fdf``, ``.fff``, ``.ffr``, ``.fits``, ``.fli``, ``.frm``, |
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| ``.gel``, ``.grey``, ``.hdr``, ``.hdr``, ``.hdr``, ``.hdr``, ``.hed``, ``.his``, ``.htd``, |
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| ``.htd``, ``.hx``, ``.i2i``, ``.ics``, ``.ids``, ``.im3``, ``.img``, ``.img``, ``.ims``, |
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| ``.inr``, ``.ipl``, ``.ipm``, ``.ipw``, ``.j2k``, ``.jp2``, ``.jpf``, ``.jpk``, ``.jpx``, |
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| ``.klb``, ``.l2d``, ``.labels``, ``.lei``, ``.lif``, ``.liff``, ``.lim``, ``.lms``, |
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| ``.lsm``, ``.map``, ``.mdb``, ``.mnc``, ``.mng``, ``.mod``, ``.mov``, ``.mrc``, |
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| ``.mrcs``, ``.mrw``, ``.msr``, ``.msr``, ``.mtb``, ``.mvd2``, ``.naf``, ``.nd``, |
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| ``.nef``, ``.nhdr``, ``.nii``, ``.nii.gz``, ``.nrrd``, ``.obf``, ``.obsep``, ``.oib``, |
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| ``.oif``, ``.oir``, ``.ome``, ``.ome.btf``, ``.ome.tf2``, ``.ome.tf8``, ``.ome.tif``, |
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| ``.ome.tiff``, ``.ome.xml``, ``.par``, ``.pbm``, ``.pcoraw``, ``.pcx``, ``.pds``, |
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| ``.pgm``, ``.pic``, ``.pict``, ``.png``, ``.pnl``, ``.ppm``, ``.pr3``, ``.ps``, ``.psd``, |
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| ``.qptiff``, ``.r3d``, ``.raw``, ``.rcpnl``, ``.rec``, ``.rec``, ``.scn``, ``.scn``, ``.sdt``, |
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| ``.seq``, ``.sif``, ``.sld``, ``.sld``, ``.sm2``, ``.sm3``, ``.spc``, ``.spe``, ``.spi``, |
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| ``.st``, ``.stk``, ``.stk``, ``.stp``, ``.sxm``, ``.tfr``, ``.tga``, ``.tif``, ``.tiff``, |
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| ``.tnb``, ``.top``, ``.vff``, ``.vsi``, ``.vws``, ``.wat``, ``.wlz``, ``.wpi``, |
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| ``.xdce``, ``.xml``, ``.xqd``, ``.xqf``, ``.xv``, ``.xys``, ``.zfp``, ``.zfr``, ``.zvi`` |
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| `Complete list of file types supported by Bio-Formats <https://docs.openmicroscopy.org/bio-formats/latest/supported-formats.html>`_ |
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