Time for a quick introduction to @QuPath in tweetorial form.
First up: a little background on how QuPath differs from other great #opensource tools for #bioimageanalysis like @FijiSc & @CellProfiler - and how to get started viewing images. 1/12
qupath.github.io
First up: a little background on how QuPath differs from other great #opensource tools for #bioimageanalysis like @FijiSc & @CellProfiler - and how to get started viewing images. 1/12
qupath.github.io
QuPath's most obvious distinguishing feature is that it handles whole slide images. These are ultra-large 2D images, often up to 50 GB in size.
Whole slide images are everywhere in #digitalpathology & increasingly common in research. 2/12
Whole slide images are everywhere in #digitalpathology & increasingly common in research. 2/12
A single whole slide image can be more than 200k x 100k pixels in size & contain a huge amount of information that matters to researchers & clinicians.
The trouble is trying to wring that information out of billions of pixels. 3/12
The trouble is trying to wring that information out of billions of pixels. 3/12
The first practical difficulty encountered is that the images are just too big to read in one go... so most software can't open them. 4/12
However, the files are cleverly arranged to have the same image data broken into tiles and stored at different resolutions.
This allows QuPath (& some other applications) to selectively read only the bits needed at any one time for visualization or analysis. 5/12
This allows QuPath (& some other applications) to selectively read only the bits needed at any one time for visualization or analysis. 5/12
To see this in action, drag an image onto QuPath to open it.
Note it doesn't *have* to be big; here I've also opened a confocal z-stack, and a photo of a sketch of a cat - with help from @bioformats lots of files should just work.
Scroll to zoom in, click & drag to pan. 6/12
Note it doesn't *have* to be big; here I've also opened a confocal z-stack, and a photo of a sketch of a cat - with help from @bioformats lots of files should just work.
Scroll to zoom in, click & drag to pan. 6/12
But we're getting ahead of ourselves. If we drag an *empty folder* onto QuPath instead of an image, it will be converted to a 'project'.
Then we can add our images to the project & switching between them will be a lot easier. 7/12
Then we can add our images to the project & switching between them will be a lot easier. 7/12
The image files aren't copied - just a link - so the projects are usually quite small. It's pretty much always better to use projects to keep things organized.
Drag & drop also works to switch projects*.
*I generally couldn't be bothered with file menus, but they work too. 8/12
Drag & drop also works to switch projects*.
*I generally couldn't be bothered with file menus, but they work too. 8/12
QuPath is mostly used with brightfield & fluorescence images & it needs to know the image type for some commands.
By default, QuPath will ask you the image type every time - but that quickly becomes annoying. Fortunately, you can tell it to make its best guess instead. 9/12
By default, QuPath will ask you the image type every time - but that quickly becomes annoying. Fortunately, you can tell it to make its best guess instead. 9/12
Whichever image type you've got, QuPath has useful visualizations built-in.
For example, digitally separate the stains either via the brightness/contrast dialog or by pressing the number corresponding to the stain you want. No need to track down a special plugin. 10/12
For example, digitally separate the stains either via the brightness/contrast dialog or by pressing the number corresponding to the stain you want. No need to track down a special plugin. 10/12
Number keys work to toggle channels in multiplexed images too - or there's also a 'Channel viewer' to see them all at once. 11/12
Ok, so that's how to view stuff.
Later I'll write about how QuPath is much more than just an image viewer... but for now I'm out of gifs.
In the meantime, you can find the full docs & info about the images above at qupath.readthedocs.io 12/12
Later I'll write about how QuPath is much more than just an image viewer... but for now I'm out of gifs.
In the meantime, you can find the full docs & info about the images above at qupath.readthedocs.io 12/12
