Jupyter Notebook for ImageJ



Not yet:

>>> import matplotlib
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python2.7/site-packages/matplotlib/__init__.py", line 124, in <module>
    from matplotlib.rcsetup import (defaultParams,
  File "/usr/local/lib/python2.7/site-packages/matplotlib/rcsetup.py", line 32, in <module>
    from matplotlib.fontconfig_pattern import parse_fontconfig_pattern
  File "/usr/local/lib/python2.7/site-packages/matplotlib/fontconfig_pattern.py", line 25, in <module>
    from pyparsing import Literal, ZeroOrMore, \
ImportError: No module named pyparsing

From a comment on Stewori/JyNI#2:

scipy also seems to work basically! :dancer:
Matplotlib fails still

I don’t know scipy well so am not sure exactly which things to try. But on macOS using system Python 2.7 I did not have any trouble building the project according to the instructions. @hanslovsky had some hiccups on Linux, but the prebuilt binary works OK minus one non-fatal Java stack trace on startup.


Status update: Claire McQuin (lead CellProfiler developer) visited Madison last week, and we worked on CellProfiler+ImageJ integration inside Jupyter. You can read about what we did here. The gist is that we have working demos of calling ImageJ from Python both in-process via pyjnius, and interprocess via ImageJ Server, as well as a notebook that combines ImageJ and CellProfiler functionality.