Merge pull request #95 from qupath/0.5

0.5

Author: petebankhead

docs/deep/gpu.md

@@ -14,9 +14,9 @@ This is **only** relevant if you're using Windows or Linux with an NVIDA GPU.
 
 :::{admonition} What about Macs?
 NVIDIA GPUs are extremely uncommon in Macs (I had one in a 2013 iMac... but no more).
-More recent Macs with Apple Silicon *do* have GPU acceleration, but it is quite different.
+More recent Macs with Apple silicon *do* have GPU acceleration, but it is quite different.
 
-Currently, Apple Silicon GPU acceleration *can* work with PyTorch via Deep Java Library.
+Currently, Apple silicon GPU acceleration *can* work with PyTorch via Deep Java Library.
 Not all models work, but I have used it very successfully with [wsinfer.md](wsinfer-extension) and seen a substantial improvement in performance.
 
 The good news is that it requires *none of the awkward configuration here*.
@@ -95,7 +95,7 @@ The following sections attempt to outline the versions (as best I can figure the
 | v0.5.x | 0.24.0  | 2.10.1     | 11.3 |
 | v0.4.x | 0.20.0  | 2.7.4      | 11.2 |
 
-> Note: DJL + TensorFlow will currently not work **at all** on Apple Silicon (no matter whether you have the Intel or Apple Silicon build of QuPath... unless you build TensorFlow from source).
+> Note: DJL + TensorFlow will currently not work **at all** on Apple silicon (no matter whether you have the Intel or Apple silicon build of QuPath... unless you build TensorFlow from source).
 
 
 ## Conda environments

docs/deep/wsinfer.md

@@ -19,7 +19,7 @@ If you use WSInfer and/or this extension in a publication, please make sure to c
 
 :::{tip}
 A GPU is not required but can dramatically speed up processing.
-If you have an NVIDIA GPU and want to use it with WSInfer, you will need to install a version of CUDA compatible with PyTorch - please see [the Deep Java Library page](deep-java-library-gpu).
+If you have an NVIDIA GPU and want to use it with WSInfer, you will need to install a version of CUDA compatible with PyTorch - please see {doc}`gpu`.
 :::
 
 
@@ -103,12 +103,12 @@ However the most (potentially) exciting additional option is the {guilabel}`Pref
 The options available will depend upon your computer's capabilities (at least as far as they could be discerned by Deep Java Library):
 
 * **CPU**: This is generally the safest - and slowest - option, because it should be supported on all computers.
-* **MPS**: This stands for *Metal Performance Shaders*, and should be available on recent Apple Silicon - it is the Mac version of GPU acceleration
+* **MPS**: This stands for *Metal Performance Shaders*, and should be available on recent Apple silicon - it is the Mac version of GPU acceleration
 * **GPU**: This should appear if you have an NVIDIA GPU, CUDA... and a little bit of luck.
 
 If either MPS or GPU work for you, they should reduce the time required for inference by a *lot*.
 However configuration for GPU can be tricky, as it will depend upon other hardware and software on your computer - CUDA in particular.
-For more info, see [the Deep Java Library page](deep-java-library-gpu).
+For more info, see {doc}`gpu`.
 
 :::{admonition} PyTorch & CUDA versions
 :class: tip

docs/intro/formats.md

@@ -28,10 +28,9 @@ Bio-Formats supports most images that can be read by OpenSlide, but not all - an
 However, file formats are tricky and tend to have lots of variants. Just because a format is listed as being supported by Bio-Formats or OpenSlide doesn't mean files in that format will always open (properly) in QuPath. The following sections contain some extra details and caveats, partly based on user feedback about what does and doesn't work.
 
 :::{important}
-If you're using a QuPath build for **Apple silicon** (i.e. a recent Mac with M1/M2 processor), then you might not have OpenSlide available by default.
-Check out <https://github.com/petebankhead/homebrew-qupath> for instructions how to install this.
+If you're using a QuPath build for **Apple silicon** (i.e. a recent Mac with M1/M2/M3 processor), then you might find that *.ndpi* and *.czi* images don't work with Bio-Formats.
 
-The same link can also help if you're using another Mac or Linux computer and want to update the version of OpenSlide that QuPath uses.
+See [here](qupath-versions-for-mac) for more details and workarounds.
 :::
 
 ### Reporting problems

index.md

@@ -6,9 +6,7 @@
 :::{sidebar} New release online!
 **QuPath {{ env.config.release }}** is available at [https://qupath.github.io](https://qupath.github.io).
 
-This fixes several bugs in v0.4.0 -- including one that prevents the user being told when there's an update.
-
-Note that these docs are still being revised for the latest release.
+See what's new in the [changelog](https://github.com/qupath/qupath/blob/main/CHANGELOG.md) - or check out the [I2K YouTube video](https://www.youtube.com/watch?v=tV-BYEHVCw8).
 :::
 
 # Welcome to QuPath!
@@ -23,7 +21,7 @@ Can't install QuPath?
 : Check out {ref}`installation` for instructions & solutions to common problems
 
 Images won't open?
-: See {ref}`supported-image-formats` to find out which formats *should* work - and ways to increase this (including instructions for **Apple silicon** users to install [OpenSlide](https://openslide.org))
+: See {ref}`supported-image-formats` to find out which formats *should* work - and ways to increase this.
 
 Not sure where to begin?
 : See {ref}`first-steps` for a quick guide, before heading to {ref}`tutorials` for more details & videos