Merge pull request #49 from petebankhead/v0.4

Update introduction

conf.py

@@ -104,6 +104,8 @@
 release = '0.4.0'
 version = '0.4a1'
 
+myst_heading_anchors = 2
+
 myst_substitutions = {
 
   "rectangle": '<img src="../images/icons/Rectangle.png" />',

docs/advanced/imagej.md

@@ -1,5 +1,11 @@
 # ImageJ
 
+```{raw} html
+<div style="text-align: center; margin-bottom: 2em;">
+<iframe width="100%" height="350" src="https://www.youtube-nocookie.com/embed/xW2Ya205nvo?rel=0" frameborder="0" allow="autoplay; encrypted-media" allowfullscreen></iframe>
+</div>
+```
+
 QuPath was created by someone who was (and is) a big fan of ImageJ.
 
 Because of this, there is a considerable amount of ImageJ inspiration that has gone into QuPath's design, and a conscious decision made to try to make QuPath more immediately accessible to someone with ImageJ experience.
@@ -131,10 +137,9 @@ All other QuPath objects within the region are converted into ROIs and added to
 The names of the ROIs are also set according to how they appear in QuPath, often based upon their {doc}`classification <../concepts/classifications>`.
 In the above screenshot, the ImageJ command {menuselection}`Image --> Overlay --> To ROI Manager` was run to create the list that is shown, where each ROI's name can be seen.
 
-:::{note}
-The selected object from QuPath is only set as an ImageJ ROI if it is not a rectangle, because a rectangle would be identical to the entire image region -- so does not contain any additional, useful information.
-
-If such a 'whole image' rectangular ROI is required in ImageJ, it can easily be created on the ImageJ side with the {menuselection}`Edit --> Selection --> Select All` command.
+:::{tip}
+Since v0.4.0, you can import saved ImageJ ROIs using {menuselection}`Extensions --> ImageJ --> Import ImageJ ROIs` - or, even handier, by drag & drop onto a QuPath viewer.
+This includes both `.roi` and `RoiSet.zip` files saved through ImageJ's ROI Manager.
 :::
 
 ### Sending snapshots

docs/intro/formats.md

@@ -1,3 +1,4 @@
+(supported-image-formats)=
 # Supported image formats
 
 ## Image files
@@ -24,6 +25,13 @@ Both libraries have their own distinct advantages:
 
 Bio-Formats supports most images that can be read by OpenSlide, but not all - and therefore QuPath continues to include both libraries.
 
+:::{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.
+
+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.
+:::
+
 ### Reporting problems
 
 Despite the fantastic work of the Bio-Formats and OpenSlide developers, the use of proprietary formats throughout the field means that images often turn up that can't be opened within QuPath.
@@ -68,6 +76,13 @@ Since the release of [Bio-Formats v5.3.0](https://www.openmicroscopy.org/site/su
 
 To open CZI files that use JPEG-XR compression on **Windows**, you may also need to install the *Visual Studio 2015 C++ Redistributable* - see [here](https://www.openmicroscopy.org/site/support/bio-formats/formats/zeiss-czi.html) for more information.
 
+
+#### DICOM
+
+Bio-Formats 6.8.0 introduced support for DICOM whole slide images.
+This is available in QuPath from v0.4.0.
+
+
 #### iSyntax (Philips)
 
 iSyntax is a proprietary format, not compatible with QuPath.

docs/starting/first_steps.md

@@ -1,3 +1,4 @@
+(first-steps)=
 # First steps
 
 The following tutorial will guide you through your first steps with QuPath, and introduce you to the main features, buttons and concepts you need to get started.

docs/tutorials/index.md

@@ -1,3 +1,4 @@
+(tutorials)=
 # Tutorials
 
 ```{toctree}

index.md

@@ -1,13 +1,32 @@
+:::{image} docs/images/qupath-banner.png
+:align: center
+:width: 75%
+:::
+
 # Welcome to QuPath!
 
 This page hosts the documentation for QuPath {{ env.config.version }}.
 
-:::{sidebar} Using QuPath v0.1.2?
-The original documentation for v0.1.2 is still [available on GitHub](https://github.com/qupath/qupath/wiki).
-:::
+## Quick links
+
+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))
+
+Not sure where to begin?
+: See {ref}`first-steps` for a quick guide, before heading to {ref}`tutorials` for more details & videos
+
+Got more questions?
+: The [Scientific Community Image Forum](https://forum.image.sc/tag/qupath) is the best place to discuss QuPath with users & developers
+
+<!-- :::{sidebar} Got more questions?
+[The Scientific Community Image Forum](https://forum.image.sc/tag/qupath) is the best place to discuss QuPath with users & developers
+::: -->
 
 ```{toctree}
-:caption: 'Contents:'
+:caption: 'Main contents:'
 :maxdepth: 2
 
 docs/intro/index