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ENH+API: Add functional interface #169

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merged 12 commits into from Jun 24, 2021
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ENH+API: Add functional interface #169

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ab19c11
ENH: Add functional interface to FISSA
scottclowe Jun 4, 2021
29c2621
TST: Test functional interface
scottclowe Jun 4, 2021
2a7bc28
ENH: Add deltaf_across_trials argument to functional interface
scottclowe Jun 4, 2021
31bbd5a
DOC: Add example scripts for working with functional interface
scottclowe Jun 4, 2021
9714734
JNB: Updates to Basic usage source
scottclowe Jun 4, 2021
a8dc63d
JNB: Add notebook for functional interface
scottclowe Jun 4, 2021
8dad809
DOC: Fix typo
scottclowe Jun 4, 2021
99cb0e9
DOC: Capitalise Jupyter
scottclowe Jun 4, 2021
644274c
DOC: Add functional interface notebook and scripts to table
scottclowe Jun 4, 2021
aade85b
DOC: Change concise example to be run_fissa
scottclowe Jun 4, 2021
cf0d8a5
JNB: Change to using datetime for the output directory
scottclowe Jun 15, 2021
94f93f7
REL: Change bleeding-edge version to 1.0.dev0
scottclowe Jun 16, 2021
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42 changes: 25 additions & 17 deletions README.rst
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Expand Up @@ -56,33 +56,41 @@ A concise example of how to use FISSA is as follows.

import fissa

experiment = fissa.Experiment('path/to/tiffs', 'path/to/rois.zip', 'experiment_name')
experiment.separate()
result = fissa.run_fissa("path/to/tiffs", "path/to/rois.zip")

# The separated time series data is now available as experiment.result
experiment.result[roi_index, tiff_index][0, :]
# The decontaminated time series is now available as
# result[roi_index, tiff_index][0, :]

We also have several example notebooks for a basic worflow and more complicated
We also have several example notebooks for a basic workflow and more complicated
workflows where FISSA needs to interact with the outputs of other two-photon
calcium imaging toolboxes which can be used to automatically detect cells.

You can try out each of the example notebooks interactively in your browser on
Binder_ (note that it may take 10 minutes for Binder to boot up).

+-----------------------+-------------------------------------------------------------------------------------+---------------------------------------------------------------+
| Workflow | Jupyter Notebook | Script |
+=======================+==========================+===============================+==========================+================================+==============================+
| Basic (ImageJ_) | `NBViewer <basichtml_>`_ | `Launch Binder <basicbind_>`_ | `Download <basicdown_>`_ | `Linux/Mac <basicnixscript_>`_ | `Windows <basicwinscript_>`_ |
+-----------------------+--------------------------+-------------------------------+--------------------------+--------------------------------+------------------------------+
| With suite2p_ | `NBViewer <suitehtml_>`_ | `Launch Binder <suitebind_>`_ | `Download <suitedown_>`_ | | |
+-----------------------+--------------------------+-------------------------------+--------------------------+--------------------------------+------------------------------+
| With SIMA_ | `NBViewer <sima_html_>`_ | `Launch Binder <sima_bind_>`_ | `Download <sima_down_>`_ | | |
+-----------------------+--------------------------+-------------------------------+--------------------------+--------------------------------+------------------------------+
| With `CNMF (MATLAB)`_ | `NBViewer <cnmf_html_>`_ | `Launch Binder <cnmf_bind_>`_ | `Download <cnmf_down_>`_ | | |
+-----------------------+--------------------------+-------------------------------+--------------------------+--------------------------------+------------------------------+
+---------------------------+-------------------------------------------------------------------------------------+---------------------------------------------------------------+
| Workflow | Jupyter Notebook | Script |
+===========================+==========================+===============================+==========================+================================+==============================+
| Functional (ImageJ_) | `NBViewer <func_html_>`_ | `Launch Binder <func_bind_>`_ | `Download <func_down_>`_ | `Linux/Mac <func_nixscript_>`_ | `Windows <func_winscript_>`_ |
+---------------------------+--------------------------+-------------------------------+--------------------------+--------------------------------+------------------------------+
| Object-oriented (ImageJ_) | `NBViewer <basichtml_>`_ | `Launch Binder <basicbind_>`_ | `Download <basicdown_>`_ | `Linux/Mac <basicnixscript_>`_ | `Windows <basicwinscript_>`_ |
+---------------------------+--------------------------+-------------------------------+--------------------------+--------------------------------+------------------------------+
| With suite2p_ | `NBViewer <suitehtml_>`_ | `Launch Binder <suitebind_>`_ | `Download <suitedown_>`_ | | |
+---------------------------+--------------------------+-------------------------------+--------------------------+--------------------------------+------------------------------+
| With SIMA_ | `NBViewer <sima_html_>`_ | `Launch Binder <sima_bind_>`_ | `Download <sima_down_>`_ | | |
+---------------------------+--------------------------+-------------------------------+--------------------------+--------------------------------+------------------------------+
| With `CNMF (MATLAB)`_ | `NBViewer <cnmf_html_>`_ | `Launch Binder <cnmf_bind_>`_ | `Download <cnmf_down_>`_ | | |
+---------------------------+--------------------------+-------------------------------+--------------------------+--------------------------------+------------------------------+

.. _Binder: https://mybinder.org/v2/gh/rochefort-lab/fissa/master?filepath=examples

.. _func_bind: https://mybinder.org/v2/gh/rochefort-lab/fissa/master?filepath=examples/Basic%20usage%20-%20Functional.ipynb
.. _func_html: https://rochefort-lab.github.io/fissa/examples/Basic%20usage%20-%20Functional.html
.. _func_view: https://github.com/rochefort-lab/fissa/blob/master/examples/Basic%20usage%20-%20Functional.ipynb
.. _func_down: https://raw.githubusercontent.com/rochefort-lab/fissa/master/examples/Basic%20usage%20-%20Functional.ipynb
.. _func_nixscript: https://github.com/rochefort-lab/fissa/blob/master/examples/basic_usage_func.py
.. _func_winscript: https://github.com/rochefort-lab/fissa/blob/master/examples/basic_usage_func_windows.py

.. _basicbind: https://mybinder.org/v2/gh/rochefort-lab/fissa/master?filepath=examples/Basic%20usage.ipynb
.. _basichtml: https://rochefort-lab.github.io/fissa/examples/Basic%20usage.html
.. _basicview: https://github.com/rochefort-lab/fissa/blob/master/examples/Basic%20usage.ipynb
Expand Down Expand Up @@ -122,7 +130,7 @@ To do so, you will need to:
3. Download `a copy of the repository <download_repo_>`_, unzip it and browse
to the examples_ directory.

4. Start up a jupyter notebook server to run our notebooks ``jupyter notebook``.
4. Start up a Jupyter notebook server to run our notebooks ``jupyter notebook``.

If you're new to Jupyter notebooks, here is `an approachable tutorial`_.

Expand Down