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BodenmillerGroup / steinbock

A toolkit for processing multiplexed tissue images
https://bodenmillergroup.github.io/steinbock
MIT License
50 stars 15 forks source link

Can't locate Ilastik #143

Closed tryggest closed 2 years ago

tryggest commented 2 years ago

I am running Steinbock from my terminal on my Mac. Everything has work fine until I try to bath process the probabilities created in Ilastik steinbock classify ilastik run

I then get the error FileNotFoundError: [Errno 2] No such file or directory: ‘/opt/ilastik/run_ilastik.sh’

(Steinbock is installed trough pip)

jwindhager commented 2 years ago

The steinbock Python package does not ship with third-party software - you'll have to install Ilastik & CellProfiler yourself and provide the path to the run_ilastik.sh file to the steinbock command via command line options, or, alternatively, use the steinbock Docker container (recommended)

tryggest commented 2 years ago

Thanks for the reply @jwindhager

When I run the docker on my mac this error pops up: WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested /opt/ilastik/ilastik-meta/lazyflow/lazyflow/classifiers/__init__.py:20: UserWarning: init: Could not import tiktorch classifier warnings.warn("init: Could not import tiktorch classifier") Starting ilastik from "/opt/ilastik". QXcbConnection: Could not connect to display Annes.home:0 Fatal Python error: Aborted

jwindhager commented 2 years ago

Unfortunately, as far as I know, the current stable version of Ilastik does not run on M1 platforms