Starting a project
Should you start a project?
Well, unless you want to quickly open an image and take a look at it, the answer is “almost always.” Some features will only work in projects, many scripts will only work in projects (as exported files and folders look specifically along the “project” file path). It will also allow you to quickly and uniformly apply your script/pipeline to a large set of images.
As of 0.2.0m3, some image types with multiple scenes or sub-files will only open in projects.
To start a project you will need an empty folder.
0.1.2+ - Use the Create project button in the Project tab, select your folder.
0.2.0 - Drag an empty folder into the open QuPath window
0.2.0 - Drag a project folder OR *.qpproj file into an open QuPath window to open the project
Import options by version
I recommend placing the images you want to analyze within the project folder whenever possible. This makes the project as a whole more portable, as you can copy it onto the network, a USB drive, etc, and open it anywhere without disrupting the file path to the images.
0.1.2+ - Drag a single image into the QuPath window that has a project active. Or in the Project tab, click Import images which will allow you to navigate to the image location and select large numbers of images.
0.2.0 - Select and drag large numbers of images into an open QuPath project. Requires a project to be open, follow the dialog instructions after.
0.2.0 - BONUS - Use the Add images button to add entire projects, which can be used to create a massive multiproject project. You may want to familiarize yourself with adding Metadata to images through the Project tab if you do this. Also be aware that the deletion of objects or images will result in their deletion from the original project. You have not copied the files, you are referencing them.
New interface shown here:
Image provider: This can normally be left as default, though I have found that if I am SURE I want to use OpenSlide (certain NDPI files), I can save some time during the import process by pre-selecting OpenSlide, as QuPath doesn’t have to go through the process of trying and failing to open each image with BioFormats.
Set Image Type: I normally set this if I am importing a large set of images, since it will save me time in case QuPath gets it wrong for all of them. For one or two images I leave it blank as QuPath does usually get it right, and it is easy enough to change in the off chance a brightfield image is set as fluorescent.
Rotation: Mostly for rotating TMAs to the “correct” orientation. Clockwise.
For whole slide image formats, the Auto-generate pyramids setting will not matter, and for TIFF files without a pyramid, it is worth waiting for this as images will load VERY slowly and be clunky to use without it.
Never tried importing objects from an image file, so not sure of cases where this would be used.
Once you import an image, a project file (project.qpproj) will be generated in the project folder. You can rename this file, though in newer versions of QuPath the File->Recent projects makes use of the folder name rather than the project name, so this is not as important.
Project files themselves are the .qpproj file within the originally empty project folder. This is what you would run, or drag into an open QuPath window, or open through the file menu. You can also drag the entire project folder itself into QuPath to save a step. The data files are stored in the “data” folder, and are named based on their association with an image file in 0.1.2. In 0.2.0 each data file is stored within a numbered subfolder, and it can be tricky to figure out which image goes with which data file.
The qpdata files store all of the objects you see in the overlays (annotations, detections) in a Java serialized object. If you are doing something destructive with your data, it is sometimes a good idea to back this folder up somewhere else so you can return to a previous step if you don’t like the results after a “Run for project.”
In 0.2.0 you will get a “classifiers” folder by default, which will, at least, contain a classes.json file with a list of your current classes as seen in the Annotations tab.
Additional folders can be created (like the Images folder mentioned above) without interfering with the project itself, though I don’t recommend editing file/folder names generated by QuPath until you are comfortable with how the project structure as a whole works.