petebankhead/homebrew-qupath

Experimental homebrew tap for QuPath-related dependencies

QuPath Homebrew tap

What's this for?

This is an experimental repo to help install OpenSlide Java.

The primary motivator here is to get OpenSlide working nicely with QuPath on new Mac computers with Apple silicon. However Homebrew also works on Intel Macs and on Linux - and so gives a way to get QuPath working with the most up-to-date OpenSlide.

In the future, more library dependencies relevant to QuPath might be added to this tap.

How do I install these formulae?

First, you'll need to install Homebrew.

Then open a command prompt (generally /Applications/Utilities/Terminal.app on a Mac) and type

brew install petebankhead/qupath/openslide-java

That's it!

It might take a little while, but Homebrew should take care of the rest.

In the future, more formulae might be added. The general pattern is that, to install something, you'd type

brew install petebankhead/qupath/<formula>

Alternatively, you can type brew tap petebankhead/qupath and then brew install <formula>.

How do I get OpenSlide to work with QuPath?

After installing openslide-java, you can find where it is by typing

brew --prefix openslide-java

The path you see will depend upon the type of computer you've got, and whether you changed the default settings. Most likely, you'll see:

• /opt/homebrew/opt/openslide-java on a Mac with Apple silicon
• /usr/local/opt/openslide-java on an Intel Mac
• /home/linuxbrew/.linuxbrew/opt/openslide-java on Linux

On Mac, you'll need to find the file libopenslide-jni.jnilib (a couple of subdirectories down) and copy it to your QuPath installation. This can be done from the command prompt, using something like this (fixing paths/versions if necessary):

cp /opt/homebrew/opt/openslide-java/lib/openslide-java/libopenslide-jni.jnilib /Applications/QuPath-0.4.0.app/Contents/app

The process for Linux is much the same, just with a different file name.

Alternative for the terminally cautious

If you aren't comfortable copying files via a command prompt and prefer the familiarity of poking around in Finder, then you can try this:

• Type open $(brew --prefix openslide-java) - this should open up Finder close to the file you need
• Find libopenslide-jni.jnilib and copy it
• Find QuPath.app, then right-click on it and choose Show package contents
• Browse down to QuPath.app/Contents/app and paste libopenslide-jni.jnilib there

If there is an existing file with the same name, you can remove that so that your new Homebrew-installed version is used.

Documentation

brew help, man brew or check Homebrew's documentation.

homebrew-qupath's Issues

unclear where to paste open slide in qupath

I was able to install 0.4.3 on apple silicon. I installed openslide via homebrew. I then cp the path below.
I can't figure out where to paste the content in qupath. Please point me to the right place in readthedocs if I missed it or let me know the steps and add it to readthedoc. thanks.

cp /opt/homebrew/opt/openslide-java/lib/openslide-java/libopenslide-jni.jnilib /Applications/QuPath-0.4.0.app/Contents/app

Version: 0.4.3
Build time: 2023-02-23, 08:39
Latest commit tag: '13689128'

Java version: 17.0.6
Java vendor: Eclipse Adoptium - https://adoptium.net/
Java home: /Applications/QuPath.app/Contents/runtime/Contents/Home

Operating system: Mac OS X - 13.5
Architecture: aarch64

Number of available processors: 10

Memory already used by JVM: 76 MB
Total memory currently available: 272 MB
Max memory JVM may try to use: 32768 MB

Library path:
/Applications/QuPath.app/Contents/app

Class path:
/Applications/QuPath.app/Contents/app/qupath-app-0.4.3.jar
/Applications/QuPath.app/Contents/app/JWlz-1.4.0.jar
/Applications/QuPath.app/Contents/app/aircompressor-0.21.jar
/Applications/QuPath.app/Contents/app/api-0.20.0.jar
/Applications/QuPath.app/Contents/app/asm-5.0.4.jar
/Applications/QuPath.app/Contents/app/base-18.09.0.jar
/Applications/QuPath.app/Contents/app/cdm-core-5.3.3.jar
/Applications/QuPath.app/Contents/app/checker-qual-3.12.0.jar
/Applications/QuPath.app/Contents/app/commonmark-0.21.0.jar
/Applications/QuPath.app/Contents/app/commons-compress-1.22.jar
/Applications/QuPath.app/Contents/app/commons-io-2.7.jar
/Applications/QuPath.app/Contents/app/commons-lang-2.6.jar
/Applications/QuPath.app/Contents/app/commons-lang3-3.12.0.jar
/Applications/QuPath.app/Contents/app/commons-math3-3.6.1.jar
/Applications/QuPath.app/Contents/app/commons-text-1.10.0.jar
/Applications/QuPath.app/Contents/app/controlsfx-11.1.2.jar
/Applications/QuPath.app/Contents/app/docs/qupath-0.4.3-javadoc.jar
/Applications/QuPath.app/Contents/app/error_prone_annotations-2.11.0.jar
/Applications/QuPath.app/Contents/app/failureaccess-1.0.1.jar
/Applications/QuPath.app/Contents/app/flowless-0.7.0.jar
/Applications/QuPath.app/Contents/app/formats-api-6.12.0.jar
/Applications/QuPath.app/Contents/app/formats-bsd-6.12.0.jar
/Applications/QuPath.app/Contents/app/formats-gpl-6.12.0.jar
/Applications/QuPath.app/Contents/app/groovy-4.0.9.jar
/Applications/QuPath.app/Contents/app/groovy-jsr223-4.0.9.jar
/Applications/QuPath.app/Contents/app/groovy-xml-4.0.9.jar
/Applications/QuPath.app/Contents/app/gson-2.10.jar
/Applications/QuPath.app/Contents/app/guava-31.1-jre.jar
/Applications/QuPath.app/Contents/app/httpclient-4.5.9.jar
/Applications/QuPath.app/Contents/app/httpmime-4.5.9.jar
/Applications/QuPath.app/Contents/app/httpservices-5.3.3.jar
/Applications/QuPath.app/Contents/app/ij-1.53v.jar
/Applications/QuPath.app/Contents/app/ikonli-core-12.3.1.jar
/Applications/QuPath.app/Contents/app/ikonli-ionicons4-pack-12.3.1.jar
/Applications/QuPath.app/Contents/app/ikonli-javafx-12.3.1.jar
/Applications/QuPath.app/Contents/app/j2objc-annotations-1.3.jar
/Applications/QuPath.app/Contents/app/jackson-annotations-2.14.1.jar
/Applications/QuPath.app/Contents/app/jackson-core-2.14.1.jar
/Applications/QuPath.app/Contents/app/jackson-databind-2.14.1.jar
/Applications/QuPath.app/Contents/app/javacpp-1.5.8-macosx-arm64.jar
/Applications/QuPath.app/Contents/app/javacpp-1.5.8.jar
/Applications/QuPath.app/Contents/app/javacpp-platform-1.5.8.jar
/Applications/QuPath.app/Contents/app/javafx-base-19-mac-aarch64.jar
/Applications/QuPath.app/Contents/app/javafx-base-19-win.jar
/Applications/QuPath.app/Contents/app/javafx-base-19.jar
/Applications/QuPath.app/Contents/app/javafx-controls-19-mac-aarch64.jar
/Applications/QuPath.app/Contents/app/javafx-controls-19-win.jar
/Applications/QuPath.app/Contents/app/javafx-controls-19.jar
/Applications/QuPath.app/Contents/app/javafx-fxml-19-mac-aarch64.jar
/Applications/QuPath.app/Contents/app/javafx-fxml-19-win.jar