Bioformats installation

cellprofiler

#1

Hello! We have enjoyed using CellProfiler for several years and recently had good success in analyzing millions of images from a genome-wide shRNA screen using the Python version of CellProfiler on a cluster. The cluster was recently upgraded and we had to reinstall CellProfiler, but we are having a hard time helping it find all the modules. The cluster administrators installed the javabridge and bioformats modules with pip, but although CP is able to load the overall bioformats module when we run the program, it says it is missing bioformats.formatreader. Do you know what is the best way to solve this problem? The cluster administrators sent us this message:

We appreciate your help! I’ve copied our error message below.

Thanks,

Philip Tan
Cardiac Systems Biology Lab
University of Virginia

Updating Java dependencies using Maven.
running build_ext
skipping ‘_cpmorphology2.c’ Cython extension (up-to-date)
skipping ‘_watershed.c’ Cython extension (up-to-date)
skipping ‘_propagate.c’ Cython extension (up-to-date)
skipping ‘_filter.c’ Cython extension (up-to-date)
skipping ‘_lapjv.c’ Cython extension (up-to-date)
skipping ‘_convex_hull.c’ Cython extension (up-to-date)
skipping ‘_fastemd.cpp’ Cython extension (up-to-date)
Unable to access the X Display, is $DISPLAY set properly?
Plugin directory doesn’t point to valid folder: /nv/blue/pmt3sw/plugins
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/nv/blue/pmt3sw/CellProfiler/imagej/jars/slf4j-simple-1.7.7.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/nv/blue/pmt3sw/CellProfiler/imagej/jars/logback-classic-1.1.1.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.impl.SimpleLoggerFactory]
Traceback (most recent call last):
File “CellProfiler/CellProfiler.py”, line 985, in
main(sys.argv)
File “CellProfiler/CellProfiler.py”, line 199, in main
cp_start_vm()
File “/nv/blue/pmt3sw/CellProfiler/cellprofiler/utilities/cpjvm.py”, line 188, in cp_start_vm
import bioformats.formatreader
ImportError: No module named formatreader


#2

The administrators were able to install the correct version of the bioformats module, so it looks like the problem is solved. Thanks for your help!

Philip


#3

Ah good! No need for thanks, as we didn’t do anything directly to help :wink:

Cheers,
David