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<h1 class="mume-header" id="oasis-fast-online-deconvolution-of-calcium-imaging-data">OASIS: Fast online deconvolution of calcium imaging data</h1>
<p>Code accompanying the paper "<a href="http://journals.plos.org/ploscompbiol/article?rev=2&id=10.1371/journal.pcbi.1005423">Fast online deconvolution of calcium imaging data</a>".</p>
<p>Python: <a href="https://github.com/j-friedrich/OASIS">https://github.com/j-friedrich/OASIS</a></p>
<p>MATLAB: <a href="https://github.com/zhoupc/OASIS_matlab">https://github.com/zhoupc/OASIS_matlab</a></p>
<p><a href="https://github.com/zhoupc/OASIS_matlab/blob/master/document/FOOPSI.html">A brief summary of the FOOPSI approach for denoising & deconvolving calcium imaging</a></p>
<h2 class="mume-header" id="get-started">Get Started</h2>
<h3 class="mume-header" id="installation">Installation</h3>
<p>add OASIS function to the search path of MATLAB</p>
<p><code>>> oasis_setup</code></p>
<h3 class="mume-header" id="process-yoru-data">Process yoru data</h3>
<p>There is also a high-level function <strong>deconvolveCa.m</strong> for the ease of calling different methods. You only need to specify parameters and then denoise & deconvolve your raw trace. For example</p>
<pre data-role="codeBlock" data-info="matlab" class="language-matlab"><span class="token punctuation">[</span>c<span class="token punctuation">,</span> s<span class="token punctuation">,</span> options<span class="token punctuation">]</span> <span class="token operator">=</span> <span class="token function">deconvolveCa</span><span class="token punctuation">(</span>y<span class="token punctuation">,</span> <span class="token string">'foopsi'</span><span class="token punctuation">,</span> <span class="token string">'ar1'</span><span class="token punctuation">,</span> <span class="token string">'smin'</span><span class="token punctuation">,</span> <span class="token operator">-</span><span class="token number">3</span><span class="token punctuation">,</span> <span class="token punctuation">...</span><span class="token string">'optimize_pars'</span><span class="token punctuation">,</span> true<span class="token punctuation">,</span> <span class="token string">'optimize_b'</span><span class="token punctuation">,</span> true<span class="token punctuation">)</span>
</pre><p>In this example, we deconvolve the raw trace <span class="katex"><span class="katex-mathml"><math><semantics><mrow><mi>y</mi></mrow><annotation encoding="application/x-tex">y</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="strut" style="height:0.43056em;"></span><span class="strut bottom" style="height:0.625em;vertical-align:-0.19444em;"></span><span class="base"><span class="mord mathit" style="margin-right:0.03588em;">y</span></span></span></span> using FOOPSI model and constrain the spike size to be <span class="katex"><span class="katex-mathml"><math><semantics><mrow><mn>3</mn><mo>×</mo></mrow><annotation encoding="application/x-tex">3\times</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="strut" style="height:0.64444em;"></span><span class="strut bottom" style="height:0.72777em;vertical-align:-0.08333em;"></span><span class="base"><span class="mord">3</span><span class="mord">×</span></span></span></span> noise levels. The AR coefficients and the baseline were updated automatically.</p>
<p>For more options, check the <strong>examples/</strong> folder and see the comments in <em>deconvolveCa.m</em>.</p>
<h3 class="mume-header" id="reproduce-figures-in-the-paper">Reproduce figures in the paper</h3>
<p>You can reproduce the figures in the paper [3] using the following command (replace * with figure index).</p>
<p><code>>> run examples/paper/fig*.m</code></p>
<h2 class="mume-header" id="copyright">Copyright</h2>
<p>Pengcheng Zhou @ Colubmia University<br>
2018</p>
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