{"id":35,"date":"2020-01-20T16:10:26","date_gmt":"2020-01-20T21:10:26","guid":{"rendered":"https:\/\/www.bme.jhu.edu\/ascharles\/brains-2\/"},"modified":"2024-09-30T10:32:41","modified_gmt":"2024-09-30T14:32:41","slug":"downloads","status":"publish","type":"page","link":"https:\/\/www.bme.jhu.edu\/ascharles\/downloads\/","title":{"rendered":"Downloads"},"content":{"rendered":"<p><strong><span style=\"font-size: inherit;\">Software<\/span><\/strong><\/p>\n<ul>\n<li>GraFT GUI: Graphical user interface (and stand-alone App) for GraFT <a href=\"_wp_link_placeholder\" data-wplink-edit=\"true\">github link<\/a><\/li>\n<li>GraFT: Graph Filtered Time-trace analysis for decoding functional optical imaging. Works on dendrites, widefield, and somatic imaging.\u00a0 <a href=\"https:\/\/github.com\/adamshch\/GraFT-analysis\">github link<\/a><\/li>\n<li>Neural Anatomy and Optical Microscopy (NAOMi) simulation code. <a href=\"https:\/\/bitbucket.org\/adamshch\/naomi_sim\/src\/master\/\">bitbucket link<\/a>. Data is available here: https:\/\/osf.io\/863j9\/<\/li>\n<li>Earth-mover&#8217;s regularized dynamic filtering (EMD-DF) code (relevant <a href=\"https:\/\/ieeexplore.ieee.org\/document\/9115856\">SPL paper<\/a> &amp; <a href=\"https:\/\/arxiv.org\/abs\/1806.04674\">arxiv link<\/a>) in MATLAB is currently available via this <a href=\"https:\/\/www.bme.jhu.edu\/ascharles\/wp-content\/uploads\/2020\/07\/emddf.zip\">zip file<\/a>.<\/li>\n<li>SEUDO: Code and GUI to detect and correct false transients in calcium imaging data. (Currently in beta testing; for early access please email us at seudo@princeton.edu)<\/li>\n<li>Code to fit flexible modulated Poisson model from the <a href=\"http:\/\/www.biorxiv.org\/content\/early\/2017\/07\/19\/165670\">&#8220;Dethroning the fano factor&#8221;<\/a> paper: <a href=\"https:\/\/github.com\/adamshch\/flexibleModulatedPoisson\">GIT repository link<\/a><\/li>\n<li>Code for source separation software (Sparse convolutional iterative shape matchine; SCISM) for stereoscopic volumetric imaging: <a href=\"https:\/\/bitbucket.org\/adamshch\/scism\/src\">GIT repository link<\/a><\/li>\n<li>Statistical Dictionary Learning Library: <a href=\"https:\/\/www.bme.jhu.edu\/ascharles\/wp-content\/uploads\/2020\/01\/Dictionary_Learning_Library_v1-0.zip \">v1.zip<\/a>,<a href=\"https:\/\/www.bme.jhu.edu\/ascharles\/wp-content\/uploads\/2020\/01\/DictionaryLearning_v2.zip \">v2.zip<\/a><\/li>\n<li>Dynamic Filtering for Sparse Signals: <a href=\"https:\/\/www.bme.jhu.edu\/ascharles\/wp-content\/uploads\/2020\/01\/RWL1DF_code.zip\">.zip<\/a><\/li>\n<li>Spatial Filtering for Sparse Signals: <a href=\"https:\/\/www.bme.jhu.edu\/ascharles\/wp-content\/uploads\/2020\/01\/RWL1SF_v1.zip\">.zip<\/a><\/li>\n<li>LaTeX equation image maker for Linux (BASH shell script): <a href=\"documents\/latexit_bpp\">latexit_bpp<\/a>. Place in searched folder and use $latexit_bpp -h for help (or look in the comments).<\/li>\n<\/ul>\n<p><strong>Documents<\/strong><\/p>\n<ul>\n<li>Information on Parallel Computing with MATLAB: <a href=\"https:\/\/www.bme.jhu.edu\/ascharles\/wp-content\/uploads\/2020\/01\/MATLAB_ParDoc.pdf\">pdf<\/a><\/li>\n<li>Derivation of the Kalman Filter using a Bayesian approach: <a href=\"https:\/\/www.bme.jhu.edu\/ascharles\/wp-content\/uploads\/2020\/01\/KalmanFilterBayesDerivation.pdf\">pdf<\/a><\/li>\n<\/ul>\n<p><strong>Presentation Slides<\/strong><\/p>\n<ul>\n<li>Causal LCA presentation given at the 2011 DSP Workshop in Sedona, AZ (Presented at the best student paper competition): <a href=\"https:\/\/www.bme.jhu.edu\/ascharles\/wp-content\/uploads\/2020\/01\/2011DSPWorkshop_Presentation.pdf\">pdf<\/a><\/li>\n<li>Sparse Dynamics Presentation given at the 2011 CISS Conference on March 23rd, 2011 in Baltimore, MD: <a href=\"https:\/\/www.bme.jhu.edu\/ascharles\/wp-content\/uploads\/2020\/01\/2011CISS_SparseDynamics_Presentation.pdf\">pdf<\/a><\/li>\n<li>Hierarchical approach to Sparse Dynamics. Presentation given at the SPARS11 Conference on June 28th, 2011 in Edinburgh, Scotland, UK: <a href=\"https:\/\/www.bme.jhu.edu\/ascharles\/wp-content\/uploads\/2020\/01\/2011SPARS11_Presentation.pdf\">pdf<\/a><\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Software GraFT GUI: Graphical user interface (and stand-alone App) for GraFT github link GraFT: Graph Filtered Time-trace analysis for decoding functional optical imaging. Works on dendrites, widefield, and somatic imaging.\u00a0 github link Neural Anatomy and Optical Microscopy (NAOMi) simulation code. bitbucket link. Data is available here: https:\/\/osf.io\/863j9\/ Earth-mover&#8217;s regularized dynamic filtering (EMD-DF) code (relevant SPL &hellip; <\/p>\n<p class=\"link-more\"><a href=\"https:\/\/www.bme.jhu.edu\/ascharles\/downloads\/\" class=\"more-link\">Continue reading<span class=\"screen-reader-text\"> &#8220;Downloads&#8221;<\/span><\/a><\/p>\n","protected":false},"author":18,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"iawp_total_views":294,"footnotes":""},"class_list":["post-35","page","type-page","status-publish","hentry","entry"],"_links":{"self":[{"href":"https:\/\/www.bme.jhu.edu\/ascharles\/wp-json\/wp\/v2\/pages\/35","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.bme.jhu.edu\/ascharles\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.bme.jhu.edu\/ascharles\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.bme.jhu.edu\/ascharles\/wp-json\/wp\/v2\/users\/18"}],"replies":[{"embeddable":true,"href":"https:\/\/www.bme.jhu.edu\/ascharles\/wp-json\/wp\/v2\/comments?post=35"}],"version-history":[{"count":11,"href":"https:\/\/www.bme.jhu.edu\/ascharles\/wp-json\/wp\/v2\/pages\/35\/revisions"}],"predecessor-version":[{"id":1107,"href":"https:\/\/www.bme.jhu.edu\/ascharles\/wp-json\/wp\/v2\/pages\/35\/revisions\/1107"}],"wp:attachment":[{"href":"https:\/\/www.bme.jhu.edu\/ascharles\/wp-json\/wp\/v2\/media?parent=35"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}