fafa87/cellstar

Algorithm for round cells identification in the brightfield microscopy images.

cellstar's Issues

Incompatible with python3

There are tons of incompatibilities with python3. I am trying to fix them but without a better understanding of the whole project, a dumb translation might not be ideal. Any plans for python3 support?

Add simple usage script to readme

Tiled examples are missing from readme

problem with pip install

Hi, i have an issue with installing your great package into venv with pip on Windows
I am going with
pip install cellstar
and get this error
Collecting matplotlib<=2.2.5 (from cellstar)
Using cached matplotlib-2.2.5.tar.gz (36.7 MB)
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error

× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [61 lines of output]
============================================================================
Edit setup.cfg to change the build options

  BUILDING MATPLOTLIB
              matplotlib: yes [2.2.5]
                  python: yes [3.9.9 (tags/v3.9.9:ccb0e6a, Nov 15 2021,
                          18:08:50) [MSC v.1929 64 bit (AMD64)]]
                platform: yes [win32]

  REQUIRED DEPENDENCIES AND EXTENSIONS
                   numpy: yes [not found. pip may install it below.]
        install_requires: yes [handled by setuptools]
                  libagg: yes [pkg-config information for 'libagg' could not
                          be found. Using local copy.]
                freetype: no  [The C/C++ header for freetype
                          (freetype2\ft2build.h) could not be found.  You may
                          need to install the development package.]
                     png: no  [The C/C++ header for png (png.h) could not be
                          found.  You may need to install the development
                          package.]
                   qhull: yes [pkg-config information for 'libqhull' could not
                          be found. Using local copy.]

  OPTIONAL SUBPACKAGES
             sample_data: yes [installing]
                toolkits: yes [installing]
                   tests: no  [skipping due to configuration]
          toolkits_tests: no  [skipping due to configuration]

  OPTIONAL BACKEND EXTENSIONS
                  macosx: no  [Mac OS-X only]
                  qt5agg: no  [PySide2 not found; PyQt5 not found]
                  qt4agg: no  [PySide not found; PyQt4 not found]
                 gtk3agg: no  [Requires pygobject to be installed.]
               gtk3cairo: no  [Requires cairocffi or pycairo to be installed.]
                  gtkagg: no  [Requires pygtk]
                   tkagg: yes [installing; run-time loading from Python Tcl /
                          Tk]
                   wxagg: no  [requires wxPython]
                     gtk: no  [Requires pygtk]
                     agg: yes [installing]
                   cairo: no  [cairocffi or pycairo not found]
               windowing: yes [installing]

  OPTIONAL LATEX DEPENDENCIES
                  dvipng: no
             ghostscript: no
                   latex: no
                 pdftops: no

  OPTIONAL PACKAGE DATA
                    dlls: no  [skipping due to configuration]

  ============================================================================
                          * The following required packages can not be built:
                          * freetype, png
                          * Please check http://gnuwin32.sourceforge.net/packa
                          * ges/freetype.htm for instructions to install
                          * freetype
                          * Please check http://gnuwin32.sourceforge.net/packa
                          * ges/libpng.htm for instructions to install png
  [end of output]

i am using pycharm, python 3.9. I am really new in python. Can you help me, please?
I also have tried to install matlab package, but have not found
Our team really appreciate your work, and we hope we can try it by ourselves

Thanks for answering!

Cellstar tutorial for directly using it from python

Hello Fafa87,

Thank you very much for providing python implementation of cell star algorithm. However, it would be very valuable if you could provide us some example cases on how to use cellstar directly from python without relying on cell profiler.

Thank you!
Warm regards,
Varshit Dusad