Add info about open uri

qupath · Sep 12, 2020 · eba498e · eba498e
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diff --git a/conf.py b/conf.py
@@ -83,5 +83,5 @@
 
 html_favicon = 'docs/images/QuPath.ico'
 
-release = '0.2.2'
+release = '0.2.3'
 version = '0.2'
diff --git a/docs/intro/citing.md b/docs/intro/citing.md
@@ -26,7 +26,7 @@ The following key indicates what, if anything, was cited in the main references
 
 ### Contents
 
-* [2020](#2020) (161)
+* [2020](#2020) (164)
 * [2019](#2019) (144)
 * [2018](#2018) (48)
 * [2017](#2017) (5)
@@ -121,9 +121,7 @@ https://doi.org/10.1016/j.ultrasmedbio.2020.07.004 📗
 
 1. Frangež, Z. et al. (2020). BIF-1 inhibits both mitochondrial and glycolytic ATP production: its downregulation promotes melanoma growth. **Oncogene**. https://doi.org/10.1038/s41388-020-1339-8 📗
 
-1. Kaalund, S. S. et al. (2020). Locus coeruleus pathology in progressive supranuclear palsy, and its relation to disease severity. **Acta Neuropathologica Communications**. https://doi.org/10.1186/s40478-020-0886-0 😞
-
-1. Karn, T. et al. (2020). A Small Hypoxia Signature Predicted pCR Response to Bevacizumab in the Neoadjuvant GeparQuinto Breast Cancer Trial. **Clinical Cancer Research**. https://doi.org/10.1158/1078-0432.CCR-19-1954 📗
+1. Ghasemi, F. et al. (2020). High MHC-II expression in Epstein–Barr virus-associated gastric cancers suggests that tumor cells serve an important role in antigen presentation. **Scientific Reports**. https://doi.org/10.1038/s41598-020-71775-4 📗
 
 1. Gil, K. N. et al. (2020). Rorqual whale nasal plugs: protecting the respiratory tract against water entry and barotrauma. **Journal of Experimental Biology**. https://doi.org/10.1242/jeb.219691 📗
 
@@ -172,6 +170,8 @@ https://doi.org/10.1016/j.canlet.2020.05.001 😞
 
 1. Jung, S. et al. (2020). Seizure-induced neuronal apoptosis is related to dysregulation of the RNA-edited GluR2 subunit in the developing mouse brain. **Brain Research**. https://doi.org/10.1016/j.brainres.2020.146760 😞
 
+1. Kaalund, S. S. et al. (2020). Locus coeruleus pathology in progressive supranuclear palsy, and its relation to disease severity. **Acta Neuropathologica Communications**. https://doi.org/10.1186/s40478-020-0886-0 😞
+
 1. Kalish, B. T. et al. (2020). Single-nucleus RNA sequencing of mouse auditory
 cortex reveals critical period triggers and brakes. **PNAS**. https://doi.org/10.1073/pnas.1920433117 📗
 
@@ -271,6 +271,10 @@ effusions in brachycephalic dogs. **Journal of Veterinary Internal Medicine**. h
 
 1. Ottley, E. C. et al. (2020). Greater utility of molecular subtype rather than epithelial‐to‐mesenchymal transition (EMT) markers for prognosis in high‐risk non‐muscle‐invasive (HGT1) bladder cancer. **Journal of Pathology: Clinical Research**. https://doi.org/10.1002/cjp2.167 📗
 
+1. Owens, R. et al. (2020). Comparison of different anti‐Ki67 antibody clones and hot‐spot sizes for assessing proliferative index and grading in pancreatic neuroendocrine tumours using manual and image analysis. **Histopathology**. https://doi.org/10.1111/his.14200 📗
+
+1. Patel, K. S. et al. (2020). Decorin expression is associated with predictive diffusion MR phenotypes of anti-VEGF efficacy in glioblastoma. **Scientific Reports**. https://doi.org/10.1038/s41598-020-71799-w 📗
+
 1. Peluso, M. O. et al. (2020). The Fully human anti-CD47 antibody SRF231 exerts dual-mechanism antitumor activity via engagement of the activating receptor CD32a. **Journal for Immunotherapy of Cancer**. https://doi.org/10.1136/jitc-2019-000413 📗
 
 1. Pilot, T. et al. (2020). Heat shock and HSP70 regulate 5-FU-mediated caspase-1 activation in myeloid-derived suppressor cells and tumor growth in mice. **Journal for ImmunoTherapy of Cancer**. http://dx.doi.org/10.1136/jitc-2019-000478 😞
@@ -358,6 +362,8 @@ multiple intestinal neoplasia (Min) mice. **International Journal of Experimenta
 
 1. Yang, T. et al. (2020). Small-molecule modulation of the p75 neurotrophin receptor inhibits a wide range of tau molecular pathologies and their sequelae in P301S tauopathy mice. **Acta Neuropathologica Communications**. https://doi.org/10.1186/s40478-020-01034-0 😞
 
+1. Yu, M. et al. (2020). Islet transplantation in the subcutaneous space achieves long-term euglycaemia in preclinical models of type 1 diabetes. **Nature Metabolism**. https://doi.org/10.1038/s42255-020-0269-7 📗
+
 1. Zhang, G. et al. (2020). Based on Histogram Analysis: ADC<sub>aqp</sub> Derived from Ultra-high b-Value DWI could be a Non-invasive Specific Biomarker for Rectal Cancer Prognosis. **Scientific Reports**. https://doi.org/10.1038/s41598-020-67263-4 📗
 
 1. Zhu, L. et al. (2020). Focused ultrasound for safe and effective release of brain tumor biomarkers into the peripheral circulation. **PLOS ONE**. https://doi.org/10.1371/journal.pone.0234182 📗

diff --git a/docs/intro/formats.rst b/docs/intro/formats.rst
@@ -4,6 +4,10 @@ Supported image formats
 
 .. include:: ../tools.txt
 
+===========
+Image files
+===========
+
 QuPath can be used with a wide range of image formats, including many whole slide formats, thanks to two essential open source libraries:
 
 * **Bio-formats**: https://docs.openmicroscopy.org/bio-formats
@@ -84,7 +88,7 @@ iSyntax (Philips)
 iSyntax is a proprietary format, not compatible with QuPath.
 We are unaware of any open source library capable of reading iSyntax files.
 
-.. TIP::
+.. tip::
   See `here <https://www.glencoesoftware.com/blog/2019/12/09/converting-whole-slide-images-to-OME-TIFF.html>`__ for a blog post from Glencoe Software about converting iSyntax to OME-TIFF.
 
 
@@ -102,7 +106,7 @@ The reasons why Bio-Formats and OpenSlide do not offer better MRXS support may b
 * https://blog.openmicroscopy.org/file-formats/community/2016/01/06/format-support/
 * https://lists.andrew.cmu.edu/pipermail/openslide-users/2012-July/000377.html
 
-.. TIP::
+.. tip::
   See `here <https://www.glencoesoftware.com/blog/2019/12/09/converting-whole-slide-images-to-OME-TIFF.html>`__ for a blog post from Glencoe Software about converting .mrxs to OME-TIFF.
 
 NDPI (Hamamatsu)
@@ -122,3 +126,50 @@ Consequently, although OpenSlide and Bio-Formats support many TIFF files, it is
 
 Perhaps the most common reason for this is that the file does not contain pyramidal layers, or these layers cannot be automatically recognized.
 This is one reason why well-supported, open formats should generally be preferred (e.g. OME-TIFF).
+
+
+========
+Open URI
+========
+
+QuPath is not limited to working with image files stored locally.
+
+:menuselection:`File --> Open URI...` provides a way to access some images stored elsewhere, *however* extensions are needed to support different kinds of image server.
+A few such extensions exist already, hopefully more will be created in the future by QuPath users.
+
+
+OMERO
+=====
+
+QuPath includes a built-in extension to work with whole slide images hosted through `OMERO <https://www.openmicroscopy.org/omero/>`_.
+
+To use it, simply find the image you want through the OMERO web viewer, copy the URI, and paste it into the :menuselection:`File --> Open URI...` dialog in QuPath.
+
+There is some additional documentation from the OMERO team in the `OMERO Guide <https://omero-guides.readthedocs.io/en/latest/qupath/docs/>`_. 
+
+.. warning::
+
+  OMERO support is via the web API.
+  This results in several limitations:
+
+  * Only RGB images are supported
+  * Image tiles are JPEG compressed
+
+  Essentially, QuPath is requesting image tiles in the same way as the OMERO web viewer.
+
+.. tip::
+
+  QuPath's OMERO support will be improved in future releases.
+  It is already possible to add URLs in a variety of formats that OMERO can provide.
+
+  This makes it possible to import multiple images -- even including some annotations -- to a QuPath :doc:`project <../tutorials/projects>` in one go.
+
+Community extensions
+====================
+
+Extensions have been developed to link QuPath with other image management systems, including:
+
+* **Google Cloud API:** https://github.com/GoogleCloudPlatform/qupath-chcapi-extension
+* **SlideScore:** https://github.com/SlideScore/qupath-extension-slidescore
+
+Note that these are external extensions that have not been tested and cannot be supported by the QuPath developers -- if you have any questions about their use, it is best to contact whoever maintains the relevant extension.
diff --git a/docs/reference/faqs.rst b/docs/reference/faqs.rst
@@ -232,6 +232,13 @@ QuPath depends on other open source readers to support images of different types
 See :doc:`../intro/formats` for details about which formats are supported, and to what extent.
 
 
+:menuselection:`File --> Open URI...` doesn't work for me!
+==========================================================
+
+:menuselection:`File --> Open URI...` requires a compatible extension needs to read images hosted remotely.
+See :ref:`Open URI` for more details.
+
+
 Why does my image open but look weird?
 ======================================