{ "info": { "author": "Sander Keemink & Scott Lowe", "author_email": "swkeemink@scimail.eu", "bugtrack_url": null, "classifiers": [ "Natural Language :: English", "Programming Language :: Python", "Topic :: Scientific/Engineering" ], "description": "|Gitter| |Travis| |Documentation| |Codecov| |Coveralls|\n\n\nFISSA\n=====\n\nFISSA (Fast Image Signal Separation Analysis) is a Python library for\ndecontaminating somatic signals from two-photon calcium imaging data. It\ncan read images in tiff format and ROIs in zips as exported by ImageJ;\nor operate with numpy arrays directly, which can be produced by\nimporting files stored in other formats.\n\nFor details of the algorithm, please see our `companion\npaper `__ published in\nScientific Reports.\n\nFISSA is compatible with both Python 2.7 and Python 3.5+. Using Python 3\nis strongly encouraged, as Python 2 will no longer be `maintained\nstarting January 2020 `__.\n\nFISSA has been tested on Ubuntu 17.04 and on Windows Windows 10 with the\n`Anaconda `__ distribution.\n\nDocumentation, including the full API, is available online at\n``_.\n\nIf you encounter a specific problem please `open a new\nissue `__. For\ngeneral discussion and help with installation or setup, please see the\n`Gitter chat `__.\n\nUsage\n-----\n\nA general tutorial on the use of FISSA can be found at:\nhttps://rochefort-lab.github.io/fissa/examples/Basic%20usage.html\n\nAn example workflow with another Python toolbox (SIMA):\nhttps://rochefort-lab.github.io/fissa/examples/SIMA%20example.html\n\nAn example workflow importing data exported from a MATLAB toolbox\n(cNMF):\nhttps://rochefort-lab.github.io/fissa/examples/cNMF%20example.html\n\nThese notebooks can also be run on your own machine. To do so, you will\nneed to `download a copy of the\nrepository `__,\nunzip it and browse to the `examples `__ directory. Then,\nstart up a jupyter notebook server to run our notebooks. If you're new\nto jupyter notebooks, an approachable tutorial can be found at\nhttps://www.datacamp.com/community/tutorials/tutorial-jupyter-notebook.\n\nInstallation\n------------\n\nInstallation on Windows\n~~~~~~~~~~~~~~~~~~~~~~~\n\nBasic prerequisites\n^^^^^^^^^^^^^^^^^^^\n\nDownload and install, in the following order:\n\n- (for Python 2.7 only) Microsoft Visual C++ Compiler for Python 2.7:\n https://www.microsoft.com/en-us/download/details.aspx?id=44266\n\n- Python 2.7 or 3.5+ (recommended) Anaconda as the Python environment,\n available from https://www.anaconda.com/download/.\n\nInstalling FISSA\n^^^^^^^^^^^^^^^^\n\nOpen ``Anaconda Prompt.exe``, which can be found through the Windows\nstart menu or search, and type or copy-paste (by right clicking) the\nfollowing:\n\n::\n\n conda install -c conda-forge shapely tifffile\n\nThen, install FISSA by running the command\n\n::\n\n pip install fissa\n\nTo test if FISSA has been installed, enter the command\n\n::\n\n python\n\nto go into the Python environment. Then type\n\n::\n\n import fissa\n\nIf no errors show up, FISSA is now installed. You can leave Python by\ntyping ``exit()``.\n\nIf you want to use the interactive plotting from the notebooks, you\nshould also install the HoloViews plotting toolbox, as follows\n\n::\n\n conda install -c ioam holoviews\n\nSee `usage <#usage>`__ above for details on how to use FISSA.\n\nInstallation on Linux\n~~~~~~~~~~~~~~~~~~~~~\n\nBefore installing FISSA, you will need to make sure you have all of its\ndependencies (and the dependencies of its dependencies) installed.\n\nHere we will outline how to do all of these steps, assuming you already\nhave both Python and pip installed. It is highly likely that your Linux\ndistribution ships with these.\n\nDependencies of dependencies\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n- `scipy `__ requires a `Fortran\n compiler and\n BLAS/LAPACK/ATLAS `__.\n\n- `shapely `__ requires GEOS.\n\n- `Pillow `__>=3.0.0 effectively\n requires a JPEG library.\n\nThese packages can be installed on *Debian/Ubuntu* with the following\nshell commands.\n\n.. code:: bash\n\n sudo apt-get update\n sudo apt-get install gfortran libopenblas-dev liblapack-dev libatlas-dev libatlas-base-dev\n sudo apt-get install libgeos-dev\n sudo apt-get install libjpeg-dev\n\n.. installing-fissa-1:\n\nInstalling FISSA\n^^^^^^^^^^^^^^^^\n\nFor normal usage of FISSA, you can install the latest release version on\nPyPI using pip:\n\n::\n\n pip install fissa\n\nTo also install fissa along with the dependencies required to run our\nsample notebooks (which include plots rendered with holoviews) you\nshould run the following command:\n\n::\n\n pip install fissa['plotting']\n\nAfterwards, you can test to see if FISSA is install by running the\ncommand\n\n::\n\n python\n\nto start an interactive python session. Then run\n\n::\n\n import fissa\n\nat the python command prompt.\n\nIf no errors show up, FISSA is now installed. You can leave the\ninteractive python session with the ``exit()`` command, or CTRL+D.\n\nFolder Structure\n----------------\n\ncontinuous_integration/\n~~~~~~~~~~~~~~~~~~~~~~~\n\nContains files necessary for deploying tests on continuous integration\nservers. Users should ignore this directory.\n\nexamples/\n~~~~~~~~~\n\nContains example code. You can load the notebooks as .ipynb directly in\nGitHub, or on your system if you know how to use jupyter notebooks.\n\nexamples/exampleData/\n~~~~~~~~~~~~~~~~~~~~~\n\nContains example data. It a zipfile with region of interests from\nImageJ. It also contains three tiff stacks, which have been downsampled\nand cropped from full data from the Rochefort lab.\n\n.. fissa-1:\n\nfissa/\n~~~~~~\n\nContains the toolbox.\n\nfissa/tests/\n~~~~~~~~~~~~\n\nContains tests for the toolbox, which are run to ensure it will work as\nexpected.\n\nCiting FISSA\n------------\n\nIf you use FISSA for your research, please cite the following paper in\nany resulting publications:\n\nS. W. Keemink, S. C. Lowe, J. M. P. Pakan, E. Dylda, M. C. W. van\nRossum, and N. L. Rochefort. FISSA: A neuropil decontamination toolbox\nfor calcium imaging signals, *Scientific Reports*, **8**\\ (1):3493,\n2018.\n`DOI:10.1038/s41598-018-21640-2 `__.\n\nFor your convenience, the FISSA package ships with a copy of this\ncitation in bibtex format, available at\n`citation.bib `__.\n\nLicense\n-------\n\nUnless otherwise stated in individual files, all code is Copyright (c)\n2015, Sander Keemink, Scott Lowe, and Nathalie Rochefort. All rights\nreserved.\n\nThis program is free software; you can redistribute it and/or modify it\nunder the terms of the GNU General Public License as published by the\nFree Software Foundation; either version 2 of the License, or (at your\noption) any later version.\n\nThis program is distributed in the hope that it will be useful, but\nWITHOUT ANY WARRANTY; without even the implied warranty of\nMERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General\nPublic License for more details.\n\nYou should have received a copy of the GNU General Public License along\nwith this program. 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