Node CellProfiler Pipeline Executor with CP 3.0 and Ubuntu environment

KNIME Extensions
1

Hi,

I’m trying to use CellProfiler Integration but without success !! I’ve an ubuntu 16.04 and a CellProfiler version 3.0.0 installed. The node CellProfiler Pipeline Executor doesn’t work with this version of CellProfiler. The console displays python: can’t open file ‘/opt/CellProfiler/cellprofiler/CellProfiler.py’ Does this node working only with the version 2 of CP ?

Best regards,

2

Hi @Cedunia,

It supports both CellProfiler 2 and CellProfiler 3.

Which version of KNIME and the CellProfiler integration are you running? You can check this via Help > About KNIME Analytics Platform > Installation Details and search for CellProfiler in the text field at the top.

Have you set the correct path to your local CP3 installation in File > Preferences > KNIME > Image Processing Plugin > CellProfiler?

Best,
Stefan

3

I’m using KNIME Analytics Platform 3.7.0.v201812041331 and CellProfiler Integration 0.3.3.v201712041656.

yes i have. have a CP3 installation into /opt/Cellprofiler/cellprofiler and i haven’t a CellProfiler.py file. I have a bin or executable file cellprofiler into /usr/local/bin

Best,

4

I have to take this back (at least to some extent).

Could you please copy this file over to the /opt/CellProfiler/cellprofiler and rename it to CellProfiler.py:

cp /usr/local/bin/cellprofiler /opt/CellProfiler/cellprofiler/CellProfiler.py

Now try to execute a CellProfiler Pipeline Executor.

Best,
Stefan

5

I’ve got a new warning; the node receives a warning message from KNIP but doesn’t cancel at all.

WARN KNIPLogService Traceback (most recent call last):
WARN KNIPLogService File “/opt/CellProfiler/cellprofiler/CellProfiler.py”, line 6, in
WARN KNIPLogService from pkg_resources import load_entry_point
WARN KNIPLogService File “/home/cedric/anaconda3/lib/python3.6/site-packages/pkg_resources/init.py”, line 3105, in
WARN KNIPLogService @_call_aside
WARN KNIPLogService File “/home/cedric/anaconda3/lib/python3.6/site-packages/pkg_resources/init.py”, line 3089, in _call_aside
WARN KNIPLogService f(*args, **kwargs)
WARN KNIPLogService File “/home/cedric/anaconda3/lib/python3.6/site-packages/pkg_resources/init.py”, line 3118, in _initialize_master_working_set
WARN KNIPLogService working_set = WorkingSet._build_master()
WARN KNIPLogService File “/home/cedric/anaconda3/lib/python3.6/site-packages/pkg_resources/init.py”, line 578, in _build_master
WARN KNIPLogService ws.require(requires)
WARN KNIPLogService File “/home/cedric/anaconda3/lib/python3.6/site-packages/pkg_resources/init.py”, line 895, in require
WARN KNIPLogService needed = self.resolve(parse_requirements(requirements))
WARN KNIPLogService File “/home/cedric/anaconda3/lib/python3.6/site-packages/pkg_resources/init.py”, line 781, in resolve
WARN KNIPLogService raise DistributionNotFound(req, requirers)
WARN KNIPLogService pkg_resources.DistributionNotFound: The ‘CellProfiler’ distribution was not found and is required by the application

Best,

6

Sorry that this is taking so long, @Cedunia, but I have a hard time reproducing the issue.

Can you elaborate on how exactly you have installed CellProfiler? While investigating the issue I stumbled over https://github.com/CellProfiler/CellProfiler/issues/1887 which recommends to run pip install -e . from the CellProfile source directory.

7

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