diff --git a/conf.py b/conf.py index 4bf2174..e022890 100644 --- a/conf.py +++ b/conf.py @@ -40,7 +40,7 @@ # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This pattern also affects html_static_path and html_extra_path. -exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] +exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', "env", ".env", ".venv", "README.md"] # -- Options for HTML output ------------------------------------------------- @@ -93,12 +93,14 @@ "tasklist", ] +autosectionlabel_prefix_document = True +autosectionlabel_maxdepth = 3 highlight_language = 'groovy' html_logo = 'docs/images/qupath_128.png' -html_favicon = 'docs/images/QuPath.ico' +html_favicon = 'docs/images/qupath.ico' # Variables for current QuPath version release = '0.6.0' diff --git a/docs/concepts/object_hierarchy.md b/docs/concepts/object_hierarchy.md index 839e5cc..c045683 100644 --- a/docs/concepts/object_hierarchy.md +++ b/docs/concepts/object_hierarchy.md @@ -2,11 +2,6 @@ {doc}`Objects ` in QuPath need to be stored somewhere - and that place is the *object hierarchy*. -:::{important} -The hierarchy behavior has changed in v0.2.0!
-If you are familiar with the old behavior, be sure to read {ref}`Differences from QuPath v0.1.2`. -::: - The name comes from the fact that the objects are all stored in a hierarchical, tree-like structure. This is achieved by each object having having a reference to: @@ -128,8 +123,8 @@ This is crucial because the `PathObjectHierarchy` class uses spatial caching and In QuPath v0.1.2, the hierarchy was resolved automatically (without asking) and this was *essential* to make sense of the measurements. -The behavior of the object hierarchy has changed in QuPath v0.2.0, with the aim of making the software faster, more powerful, and more intuitive. -In v0.2.0 the details of the hierarchy can very often be ignored, and exists only to support sophisticated workflows where it might be needed. +The behavior of the object hierarchy changed in QuPath v0.2.0, with the aim of making the software faster, more powerful, and more intuitive. +In v0.2.0 and onwards, the details of the hierarchy can very often be ignored, and exists only to support sophisticated workflows where it might be needed. [This blog post](https://petebankhead.github.io/qupath/2019/11/17/changing-the-hierarchy.html) describes the reasons why it changed. To read about the earlier behavior see [Object hierarchies](https://github.com/qupath/qupath/wiki/Object-hierarchies) on the old wiki. diff --git a/docs/deep/stardist.md b/docs/deep/stardist.md index f5b56d3..5fa269d 100644 --- a/docs/deep/stardist.md +++ b/docs/deep/stardist.md @@ -403,7 +403,7 @@ def stardist = StarDist2D.builder(pathModel) Furthermore, we can use preprocessing to convert images to become more compatible with pretrained StarDist models. For example, `dsb2018_heavy_augment.pb` works very well for fluorescence microscopy images, but only supports a single input channel. -However, by applying {ref}`color deconvolution` as preprocessing we can convert a 3-channel brightfield image to a single-channel image that *looks* much more like a fluorescence image. +However, by applying {ref}`color deconvolution` as preprocessing we can convert a 3-channel brightfield image to a single-channel image that *looks* much more like a fluorescence image. If needed, we can add extra things like filters to reduce noise as well. ```groovy diff --git a/docs/deep/wsinfer.md b/docs/deep/wsinfer.md index be14b9b..64b6f32 100644 --- a/docs/deep/wsinfer.md +++ b/docs/deep/wsinfer.md @@ -153,7 +153,7 @@ wsinfer The QuPath WSInfer extension is scriptable, which makes it much easier to apply across multiple images. -When a model is run, the command parameters are stored in the [workflow](workflows) so that a [script can be generated automatically](workflows-to-scripts). +When a model is run, the command parameters are stored in the [workflow](docs/scripting/workflows:Workflows) so that a [script can be generated automatically](docs/scripting/workflows_to_scripts:Workflows to scripts). An example script would be diff --git a/docs/intro/installation.md b/docs/intro/installation.md index 8b03e35..1b4e0d4 100644 --- a/docs/intro/installation.md +++ b/docs/intro/installation.md @@ -23,7 +23,7 @@ QuPath requires 64-bit Windows. Running QuPath on 32-bit Windows is not supported. ::: -#### Installing the Windows .msi package +### Installing the Windows .msi package Double-click to launch the installer. Windows tries to protect you from software it does not know, so you'll probably see a scary-looking warning whenever the QuPath installer is first run: @@ -57,7 +57,7 @@ If the QuPath installer does not start at all, you may not have administrator pr Try downloading the `.zip` file instead, which should not need such privileges. ::: -#### Installing the Windows .zip package +### Installing the Windows .zip package Right-click on the .zip file and choose to extract all the contents. This should give you a normal folder containing QuPath's files. @@ -70,7 +70,7 @@ The first time you try this, you might see similar warning dialogs to those show On Windows, you can either run `QuPath.exe` or `QuPath (console).exe`. The difference is that `QuPath (console).exe` will also open a small window that contains QuPath's log messages. -The console can be useful for debugging problems, or when using the {ref}`Command line`. +The console can be useful for debugging problems, or when using the {ref}`docs/advanced/command_line:Command line`. ::: :::{admonition} QuPath won't launch! @@ -170,4 +170,4 @@ QuPath for Linux was compiled on Ubuntu - with best efforts made to include all ## Running from source -If all else fails, you can try [](building) - which should work on Windows, macOS and Linux. \ No newline at end of file +If all else fails, you can try [](building) - which should work on Windows, macOS and Linux. diff --git a/docs/reference/building.md b/docs/reference/building.md index 16da98e..8f352d7 100644 --- a/docs/reference/building.md +++ b/docs/reference/building.md @@ -65,7 +65,7 @@ Example of command line build success **That's it!** You can find QuPath inside the `./build/dist/` subdirectory. -If it *didn't* go so well, check out [](#Troubleshooting). +If it *didn't* go so well, check out {ref}`docs/reference/building:Troubleshooting`. :::{admonition} Which Java version do I need? :class: tip @@ -181,7 +181,7 @@ Check out the docs associated with the specific version if this is the case. (building-qupath-fiji)= ## Building with Fiji By default, QuPath embeds a version of [ImageJ](https://imagej.net/software/imagej/). -This allows you to [send image regions to ImageJ, and even use custom ImageJ plugins](ImageJ). +This allows you to [send image regions to ImageJ, and even use custom ImageJ plugins](docs/advanced/imagej:ImageJ). [Fiji](https://fiji.sc) is a special distribution of ImageJ that contains a *lot* of custom plugins, and many extra features and other changes. diff --git a/docs/reference/faqs.md b/docs/reference/faqs.md index d231f76..8ba2708 100644 --- a/docs/reference/faqs.md +++ b/docs/reference/faqs.md @@ -131,7 +131,7 @@ It is designed so that other machine learning libraries could potentially be use ### Why do I see a warning when I try to install QuPath? -See {ref}`Installation`. +See {ref}`docs/intro/installation:Installation`. (set-max-memory)= @@ -185,11 +185,11 @@ See {doc}`../intro/formats` for details about which formats are supported, and t ### {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. +See {ref}`docs/intro/formats:Open URI` for more details. ### Why does my image open but look weird? -See {ref}`Why can't QuPath open my image?` +See {ref}`docs/reference/faqs:Why can't QuPath open my image?` ### Is it possible to view slide labels? diff --git a/docs/reference/tips_and_tricks.md b/docs/reference/tips_and_tricks.md deleted file mode 100644 index 1cd465e..0000000 --- a/docs/reference/tips_and_tricks.md +++ /dev/null @@ -1,9 +0,0 @@ -(tips-and-tricks)= -# Tips and Tricks - -This page is dedicated to sharing shortcuts that can help you work more efficiently with QuPath. -Check back often for new tips and tricks! - -If you draw an annotation you don't like and its selected, you can simply press the {kbd}`Backspace` or {kbd}`Delete` key to remove the currently selected objects. - -Most sub-windows can be quickly closed from the keyboard with {kbd}`Ctrl`/{kbd}`Cmd` + {kbd}`W` or {kbd}`Esc`. \ No newline at end of file diff --git a/docs/tutorials/density_maps.md b/docs/tutorials/density_maps.md index bb8ca55..26dcc85 100644 --- a/docs/tutorials/density_maps.md +++ b/docs/tutorials/density_maps.md @@ -20,7 +20,7 @@ In some cases, density maps can even be a replacement for {doc}`pixel_classifica :::{warning} Like most commands in QuPath, Density Maps are currently calculated only in 2D. -And, like many other commands, you should create Density Maps within a {ref}`project ` if you want to reuse them later. +And, like many other commands, you should create Density Maps within a {ref}`project ` if you want to reuse them later. ::: ## Getting started with density maps @@ -61,7 +61,7 @@ Hovering your mouse over any option should provide some help text. The {guilabel}`Object type` and {guilabel}`Main class` define which objects will contribute to the density map in some way. -Left to the defaults, the density map will make use of all detection objects (which {ref}`includes cells `) regardless of their classification. +Left to the defaults, the density map will make use of all detection objects (which {ref}`includes cells `) regardless of their classification. If I choose the {guilabel}`Main class` to be **Tumor**, then the density map will *only* include detections that are classified as **Tumor**. diff --git a/docs/tutorials/separating_stains.md b/docs/tutorials/separating_stains.md index b71122d..09230c9 100644 --- a/docs/tutorials/separating_stains.md +++ b/docs/tutorials/separating_stains.md @@ -16,7 +16,7 @@ QuPath supports images of different kinds. Some commands will work on almost any kind of image without complaint, while some need to know a bit more about the image. -This information can be provided by {ref}`setting the image type `. +This information can be provided by {ref}`setting the image type `. Typically the type will be either *Brightfield* or *Fluorescence*. @@ -118,7 +118,7 @@ The stain vectors are key to color deconvolution. They ought to give a normalized representation of the color of each 'pure' stain in the image, without regard for staining intensity. A similar color vector characterizing the background encodes what 'no stain' looks like, and also plays an important role in the calculations. -When {ref}`setting the image type ` to *Brightfield (H&E)*, *Brightfield (H-DAB)* or *Brightfield (Other)*, QuPath will set default stain vectors to characterize hematoxylin, eosin or DAB. +When {ref}`setting the image type ` to *Brightfield (H&E)*, *Brightfield (H-DAB)* or *Brightfield (Other)*, QuPath will set default stain vectors to characterize hematoxylin, eosin or DAB. However, you may see better results with some commands (e.g. *Cell detection*) by setting the stain and background vectors explicitly to better match the actual staining in the image. This requires two steps: diff --git a/index.md b/index.md index c5343e5..5fdccf7 100644 --- a/index.md +++ b/index.md @@ -13,7 +13,7 @@ To read up on the latest changes, check out the [release notes](https://github.c ## Quick links Can't install QuPath? -: Check out {ref}`installation` for instructions & solutions to common problems +: Check out {ref}`docs/intro/installation: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.