{ "info": { "author": "David N. Mashburn", "author_email": "david.n.mashburn@gmail.com", "bugtrack_url": null, "classifiers": [], "description": "SeedWater Segmenter\n===================\n\nSeedwater Segmenter (SWS) is a graphical Python program to interactively segment\nimage stacks of cells in tissue with edge-labels (aka. white outlines).\nThe interactions are entirely based on the editing of seeds,\nwhich in turn are expanded by a watershed algorithm.\nThe major difference between SWS and other tools is that you can place more than one seed per cell,\nwhich can help you adjust the boundaries of difficult cells.\n\nSWS is built on top of wxPython, matplotlib, numpy, scipy, PIL, and mahotas.\n\nAt its core, it uses a lightning-fast watershed algorithm (thanks to the mahotas project) and allows real-time updates.\nIt has a simple (if cluttered) UI and is fully interactive, even including 1-level undo.\n\nThe publication about SWS that gives all these details and more in Cytometry Part A:\n\nhttp://onlinelibrary.wiley.com/doi/10.1002/cyto.a.22034/abstract\n\nSource code is mirrored to four repositories and to PyPI:\n\n- GitHub: http://github.com/davidmashburn/SeedWaterSegmenter/\n\n- Bitbucket: http://bitbucket.org/davidmashburn/seedwatersegmenter\n\n- Gitorious: http://gitorious.org/seedwatersegmenter\n\n- Google Code: http://code.google.com/p/seedwater/\n\n- PyPI: http://pypi.python.org/pypi/SeedWaterSegmenter\n\n\nYou may also want to read the manual, but be aware that it needs updating: \"SeedWaterSegmenter V x.x Manual.txt\"\n\n----\n\nInstalling and Running\n----------------------\nSeedWater is now pure-python. In fact, with just python and setuptools installed, you could install it with just::\n \n easy_install SeedWaterSegmenter\n\nThe big caveat to this is that SeedWater also depends on a number of binary/compiled dependencies which must be installed separately, the trickiest usually being mahotas.\nIt also depends on the standard scientific python packages (like numpy, scipy, matplotlib, PIL, etc), so those must also be installed.\nPretty much any method of obtaining those should work.\n\nIn short, you will need to install all of these dependencies either with binary installers, package managers, or by compiling from source.\n\nMany great Python Distributions exist for installing Python and most of these dependencies all at once.\nMy current favorite is Anaconda which is free and works on both Windows and Mac.\n\nOne other important point is that SeedWater does NOT run on Python 3.x at this time, because not all of these dependencies have been ported over.\nFor the near future, please use Python 2.7 only.\n\nWindows:\n^^^^^^^^\nDownload and install Anaconda Python Distribution:\n http://continuum.io/downloads\n \n Download either 32 or 64 bit (to match your version of Windows).\n \n Double-click on the downloaded file and install it.\n I *highly* recommend doing a single-user (non-system-wide) install to save headaches with permissions.\n\nInstall wxPython and SeedWater Segmenter:\n Now, from the Start Menu (aka, the Windows Button) select the Anaconda Command Prompt inside the Anaconda folder.\n Here, run these two commands (and you may need to disable your antivirus before proceeding)::\n \n conda install wxpython\n pip install SeedWaterSegmenter\n\nRun SeedWater:\n Now, from this same Anaconda command prompt, you can run SeedWater with the following command::\n \n python -m SeedWaterSegmenter.SeedWaterSegmenter\n\nMake a desktop launcher (with an icon):\n To make running SeedWater easier, you can install a desktop shortcut with the included script.\n Just run one of these two command from the Anaconda Command Prompt\n (depending on whether you did a single-user or system-wide install)::\n \n python C:\\Users\\\\Anaconda\\Scripts\\create_sws_shortcut.py -install\n python C:\\Anaconda\\Scripts\\create_sws_shortcut.py -install\n\n That's it!\n\nMac OS X:\n^^^^^^^^^\nObtain a C compiler:\n Download XCode from the Mac App Store or from https://developer.apple.com/xcode/\n \n Install it and run it.\n \n To get gcc, you must install command line tools, a package for XCode.\n You can access this from: XCode menu > Preferences > Downloads.\n Check \"command line tools\" and install.\n \n Reboot your system to make sure everything is loaded.\n\nDownload and install Anaconda Python Distribution: \n http://continuum.io/downloads\n \n Download either the bash installer or the GUI installer.\n To run the bash installer, download the file to the Downloads folder and run this command in the Terminal::\n \n cd ~/Downloads\n bash Anaconda*.sh\n\n If you used the \"pkg\" download, just double-click it to install.\n \n In either case, you can then choose either a single-user of system-wide install.\n\nInstall wxPython:\n Now, open a NEW Terminal window, and run this command to install wxPython::\n \n conda install wxpython\n\n This failed for me on Mac OS X Snow Leopard, so I had to download this file\n (http://repo.continuum.io/pkgs/free/osx-64/wxpython-3.0-py27_0.tar.bz2)\n to the Downloads folder, and then run these commands::\n \n cd ~/Downloads\n conda install wxpython-3.0-py27_0.tar.bz2\n\nInstall SeedWater Segmenter:\n In the Terminal, run the following::\n \n pip install SeedWaterSegmenter\n\nRun SeedWater:\n Now you can run SeedWater with the following command, noting that you HAVE to use \"pythonw\" and not just \"python\"::\n \n pythonw -m SeedWaterSegmenter.SeedWaterSegmenter\n\nDownload the App:\n Now also, thanks to Sveinbjorn Thordarson's Platypus tool, a packaged app is available for download:\n https://github.com/davidmashburn/SeedWaterSegmenter/blob/master/MacOSX/SeedWaterSegmenterApp.zip\n \n Just extract the zip file and place the App on the Desktop or in the Applications folder.\n\n Be aware that this is only a link to the python scripts and will not work by itself without the above installation.\n\n (There is also a \".command\" file that can serve the same purpose if the App does not work at\n https://github.com/davidmashburn/SeedWaterSegmenter/blob/master/MacOSX/SeedWaterSegementer.command )\n\n That's it!\n\n\nUbuntu/Debian:\n^^^^^^^^^^^^^^\nInstall:\n Run these two commands in the terminal::\n \n sudo apt-get install python-setuptools python-wxtools python-numpy python-scipy python-matplotlib python-imaging python-xlrd python-xlwt\n sudo easy_install -U SeedWaterSegmenter\n \n Run SeedWater:\n In the terminal, run::\n \n python2.7 -m SeedWaterSegmenter.SeedWaterSegmenter\n \n (just \"python\" may also work, depending on your system)\n \n Make a desktop launcher:\n 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