Skip to content

Add QuPath instructions #454

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Add QuPath instructions #454

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
20 changes: 20 additions & 0 deletions docs/guides/user-guide.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -164,6 +164,26 @@ work via QuPath’s built-in OpenCV (if you’re very lucky), or if you
[build QuPath from source](https://qupath.readthedocs.io/en/latest/docs/reference/building.html#building)
adding the OnnxRuntime engine to DJL.

#### Instructions

1. - Download and install QuPath according to
[the instructions in the documentation](https://qupath.readthedocs.io/en/latest/docs/intro/installation.html).
- Launch QuPath.
- Install [the `bioimageio` extension](https://github.com/qupath/qupath-extension-bioimageio)
according to the instructions on [the QuPath documentation](https://qupath.readthedocs.io/en/latest/docs/intro/extensions.html).
- Optionally, install [the Deep Java Library extension](https://github.com/qupath/qupath-extension-djl/)
and use this extension to download PyTorch and TensorFlow.

2. Download and unzip a model from the BioImage Model Zoo. Version 0.1.0 of QuPath's bioimageio extension only
supports models using the 0.4.x version of the BioImageIO model spec; versions 0.2.0 onwards also
support models using 0.5.x formats.

3. Create a pixel classifier for a supported model by running the command
`Extensions -> Bioimage Model Zoo -> Create pixel classifier (Bioimage Model Zoo)` and locating the previously downloaded model zip.

4. More detailed instructions can be found at [QuPath's readthedocs BioImage Model Zoo page](https://qupath.readthedocs.io/en/latest/docs/deep/bioimage.html)


### SpotMAX
SpotMAX supports models that take a single 2D or 3D input image. There is no limit to the number of images that the model returns, however, SpotMAX will use only one. The index of the output image to be used is a user-selected parameter.

Expand Down