Commit 6935ce7d authored by Somnath, Suhas's avatar Somnath, Suhas Committed by GitHub
Browse files

Updated links and simplified a few sections

parent 98e1ca5d
......@@ -6,9 +6,12 @@ pycroscopy
What is pycroscopy?
-------------------
pycroscopy is a `python <http://www.python.org/>`_ package for image processing and scientific analysis of imaging modalities such as multi-frequency scanning probe microscopy,
scanning tunneling spectroscopy, x-ray diffraction microscopy, and transmission electron microscopy.
Classes implemented here are ported to a high performance computing platform at `Oak Ridge National Laboratory (ORNL) <http://www.ornl.gov/>`_.
pycroscopy is a `python <http://www.python.org/>`_ package for image processing and scientific analysis of imaging modalities such as multi-frequency scanning probe microscopy, scanning tunneling spectroscopy, x-ray diffraction microscopy, and transmission electron microscopy.
With `pycroscopy <https://pycroscopy.github.io/pycroscopy/>`_ we aim to:
1. provide a community-developed, open standard for data formatting
2. provide a framework for developing data analysis routines
3. significantly lower the barrier to advanced data analysis procedures by simplifying I/O, processing, visualization, etc.
To learn more about the motivation, general structure, and philosophy of pycroscopy, please read this `short introduction <https://github.com/pycroscopy/pycroscopy/blob/master/docs/pycroscopy_2017_07_11.pdf>`_.
......@@ -18,7 +21,7 @@ The package structure is simple, with 4 main modules:
1. `io`: Input/Output from custom & proprietary microscope formats to HDF5.
2. `processing`: Multivariate Statistics, Machine Learning, and Filtering.
3. `analysis`: Model-dependent analysis of information.
4. `viz`: Plotting functions and custom interactive jupyter widgets
4. `viz`: Plotting functions and interactive jupyter widgets to visualize multidimenional data
Once a user converts their microscope's data format into an HDF5 format, by simply extending some of the classes in `io`, the user gains access to the rest of the utilities present in `pycroscopy.*`.
......@@ -59,17 +62,15 @@ Compatibility
* Pycroscopy was initially developed in python 2 but all current / future development for pycroscopy will be on python 3.5+. Nonetheless, we will do our best to ensure continued compatibility with python 2.
* We currently do not support 32 bit architectures
API and Documentation
---------------------
* See our `homepage <https://pycroscopy.github.io/pycroscopy/>`_ for more information
* Our api (documentation for our functions and classes) is available `here <http://https://pycroscopy.github.io/pycroscopy/index.html/>`_
* Details regarding pycroscopy's `data format <https://github.com/pycroscopy/pycroscopy/blob/master/docs/Pycroscopy_Data_Formatting.pdf>`_ for HDF5 are also available in the docs. You can check out how we are able to represent multidimensional datasets of arbitrary sizes.
Examples and Resources
----------------------
* We use `jupyter <http://jupyter.org>`_ notebooks for our scientific workflows. This `youtube video <https://www.youtube.com/watch?v=HW29067qVWk>`_ provides a nice overview on jupyter notebooks.
* We host many `jupyter notebooks <https://github.com/pycroscopy/pycroscopy/blob/master/jupyter_notebooks/>`_ of popular scientific workflows and many of them are tied to journal publications (see below).
Getting Started
---------------
* See how we use pycroscopy for our scientific research in these `jupyter notebooks <https://github.com/pycroscopy/pycroscopy/blob/master/jupyter_notebooks/>`_. Many of them are linked to journal publications listed below.
* Please see the official `jupyter <http://jupyter.org>`_ website for more information about notebooks. This `youtube video <https://www.youtube.com/watch?v=HW29067qVWk>`_.
* See our `examples <https://pycroscopy.github.io/pycroscopy/auto_examples/index.html>`_ to get started on using and writing your own pycroscopy functions
* Videos and other tutorials are available at the `Institute For Functional Imaging of Materials <http://ifim.ornl.gov/resources.html>`_
* For more information about our functions and classes, please see our `API <https://pycroscopy.github.io/pycroscopy/pycroscopy.html>`_
* We have many translators that transform data from popular microscope data formats to pycroscopy compatible .h5 files. We also have `tutorials to get you started on importing your data to pycroscopy <https://pycroscopy.github.io/pycroscopy/auto_examples/plot_translator_tutorial.html#sphx-glr-auto-examples-plot-translator-tutorial-py>`_.
* Details regarding the defention, implementation, and guidelines for pycroscopy's `data format <https://github.com/pycroscopy/pycroscopy/blob/master/docs/Data_Format.md>`_ for `HDF5 <https://github.com/pycroscopy/pycroscopy/blob/master/docs/Pycroscopy_Data_Formatting.pdf>`_ are also available.
Journal Papers using pycroscopy
-------------------------------
......@@ -85,19 +86,16 @@ Journal Papers using pycroscopy
International conferences and workshops using pycroscopy
--------------------------------------------------------
* Aug 8 2017 @ 10:45 AM - Microscopy and Microanalysis conference - poster session
* Aug 9 2017 @ 8:30 - 10:00 AM - Microscopy and Microanalysis conference; X40 - Tutorial session on `Large Scale Data Acquisition and Analysis for Materials Imaging and Spectroscopy <http://microscopy.org/MandM/2017/program/tutorials.cfm>`_ by S. Jesse and S. V. Kalinin
* Oct 31 2017 @ 6:30 PM - American Vacuum Society conference; Session: SP-TuP1; poster 1641
* Dec 2017 - Materials Research Society conference
News
----
* Oct 31 2017 @ 6:30 PM - American Vacuum Society conference; Session: SP-TuP1; poster 1641
* Aug 9 2017 @ 8:30 - 10:00 AM - Microscopy and Microanalysis conference; X40 - Tutorial session on `Large Scale Data Acquisition and Analysis for Materials Imaging and Spectroscopy <http://microscopy.org/MandM/2017/program/tutorials.cfm>`_ by S. Jesse and S. V. Kalinin
* Aug 8 2017 @ 10:45 AM - Microscopy and Microanalysis conference - poster session
* Apr 2017 - Lecture on `atom finding <https://physics.appstate.edu/events/aberration-corrected-stem-teaching-machines-and-atomic-forge>`_
* Dec 2016 - Poster + `abstract <https://mrsspring.zerista.com/poster/member/85350>`_ at the 2017 Spring Materials Research Society (MRS) conference
Contact us
----------
* We are interested in collaborating with industry members to integrate pycroscopy into instrumentation or analysis software.
* We are interested in collaborating with industry members to integrate pycroscopy into instrumentation or analysis software and can help in exporting data to pycroscopy compatible .h5 files
* We can work with you to convert your file formats into pycroscopy compatible HDF5 files and help you get started with data analysis.
* Join our slack project at https://pycroscopy.slack.com to discuss about pycroscopy
* Feel free to get in touch with us at pycroscopy (at) gmail [dot] com
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