Install and start qupath ubuntu 20.04

Hi,

how can I install QuPath 0.2.1 on ubuntu 20.04? (I am new to ubuntu and linux in general).
I extracted the qupath folder. How am I supposed to proceed? Is there some command like “make install”?

Best,
Sophia

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If by extracted the QuPath folder you mean that you downloaded the pre-built version of QuPath you should be able to open QuPath by
CTRL + ALT + T (open terminal)

type the below to navigate to the bin folder inside the QuPath folder (change something with the specifics for the location your machine
cd /something/someting/QuPath-0.2.1/bin/

then type
./QuPath-0.2.1

Voila, QuPath should open

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Hey, thank you for your reply. I did so but this is what happened:

A fatal error has been detected by the Java Runtime Environment:

SIGSEGV (0xb) at pc=0x00007fa4857e637e, pid=19999, tid=20027

JRE version: OpenJDK Runtime Environment AdoptOpenJDK (14.0.1+7) (build 14.0.1+7)

Java VM: OpenJDK 64-Bit Server VM AdoptOpenJDK (14.0.1+7, mixed mode, tiered, g1 gc, linux-amd64)

Problematic frame:

C [libc.so.6+0x9d37e] __libc_malloc+0x11e

Core dump will be written. Default location: Core dumps may be processed with “/usr/share/apport/apport %p %s %c %d %P %E” (or dumping to /home/alex/Desktop/QuPath-0.2.1/bin/core.19999)

If you would like to submit a bug report, please visit:

https://github.com/AdoptOpenJDK/openjdk-support/issues

--------------- S U M M A R Y ------------

Command Line: -Djava.library.path=/home/alex/Desktop/QuPath-0.2.1/lib/app:/home/alex/Desktop/QuPath-0.2.1/bin -Djava.launcher.path=/home/alex/Desktop/QuPath-0.2.1/bin -XX:MaxRAMPercentage=50 qupath.QuPath

This is what it says in the error log

do i maybe have to uninstall the openjdk versions that I had installed seperately before?

it just worked now… weird.

But however, there is only half of my ram in total shown? I have 64 gb, but the max available there is 32 gb. Is there a way to fix this?

Edit: i have strange black/transparent tiles when I look at an svs file. It only goes away when I zoom in but comes back when going back to overview.

There seems to be a bug with openJDK-14-jdk from apt. I had to intall the oracle JDK to be able to build the tensorflow version of QuPath.

If you read the documentation you should be able to set the amount of RAM etc.

The tiling problem is a known issue with libpixman. See this post for a workaround

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Not sure if it helps, but if you have access to another computer you might find QuPath works better on Windows and Mac. It’s primarily developed and Windows and Mac… I rarely use Linux myself, and usually only find out about Linux-specific problems when someone reports them :slight_smile:

This is intentional to prevent QuPath being too greedy, the info @Tkilvaer refers to is at https://qupath.readthedocs.io/en/latest/docs/intro/installation.html#setup-options

Another workaround may be to specify that the ‘Image provider’ should be ‘Bio-Formats’ when adding images to a project: https://qupath.readthedocs.io/en/latest/docs/tutorials/projects.html#add-images

Actually I use Qupath on windows as well (I have a dual boot system) but I just thought that it may be useful, if QuPath and my deep learning stuff are running on the same system together aswell (which I am not so sure about now anymore :wink: ).

Thanks for the tips!

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I managed to uninstall openJDK 14 and installed oracle JDK 14.0.1, but the “tiles problem” is still there and apparently an openjdk8 version is still hiding somewhere on my system although I adjusted the path variable for oracle jdk appropriately. Dunno whether it’s worth to invest more time or just stick to the windows version on my second boot system (dual boot with windows).

Edit: thanks for tips and help so far!

The tiling thing is likely to be either related to OpenSlide (and pixman as a dependency of OpenSlide) or something actually within the SVS file itself.

If the same image works fine in Windows, then I suspect it’s the OpenSlide issue. Installing/updating the OpenSlide dependencies directly within Ubuntu may help (since QuPath is unfortunately affected by the systemwide installation on Linux more than it should be).

Alternatively, avoiding OpenSlide altogether and reading the images with Bio-Formats should avoid it.

However, for some SVS files (written by some software) parts of the image might really not be included in the image file – and then the black boxes appear at some resolutions.

Regarding JDKs…

If you’re using QuPath downloaded from the GitHub releases page (instead of building it yourself using Gradle) then the JDK shouldn’t matter - QuPath will use AdoptOpenJDK, which is included as part of the download.

Note that if you do need to install a JDK, nowadays OpenJDK is really the standard – since Oracle JDK has got some other licensing model.

There is however an additional gotcha here… if you install a JDK you probably want to ensure it uses HotSpot rather than OpenJ9. Since that has emerged as another source of crashes recently: https://github.com/qupath/qupath/issues/484#issuecomment-648053127

I personally use AdoptOpenJDK 14.0.1 with HotSpot and haven’t had trouble with it… but it should all be irrelevant for your situation if you’re using the pre-built release :slight_smile:

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the problem with the tiles got solved for me, as in another post already was mentioned by installing another version of the pixman library.

Installing version 0.40 solved it for me. The link, if someone should have the same problem.
http://www.linuxfromscratch.org/blfs/view/svn/general/pixman.html

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how can I install QuPath 0.2.1 on ubuntu 20.04? (I am new to ubuntu and linux in general).
I extracted the qupath folder. How am I supposed to proceed? Is there some command like “make install”?

This is not a problem with QuPath, but a known problem with how nautilus (the default file manager in Ubuntu Gnome) mistakes location independent executable files as shared libraries.

QuPath can be run in the terminal. Alternatively you can use dolphin as file manager.

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Good to know, thanks!