{"id":183,"date":"2013-12-02T12:49:12","date_gmt":"2013-12-02T10:49:12","guid":{"rendered":"http:\/\/titan.physx.u-szeged.hu\/~adoptim\/?page_id=183"},"modified":"2024-08-26T14:12:23","modified_gmt":"2024-08-26T12:12:23","slug":"teststorm","status":"publish","type":"page","link":"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/?page_id=183","title":{"rendered":"TestSTORM"},"content":{"rendered":"<p><a href=\"https:\/\/creativecommons.org\/licenses\/by-sa\/4.0\/\"><img loading=\"lazy\" decoding=\"async\" data-attachment-id=\"580\" data-permalink=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/?attachment_id=580\" data-orig-file=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2013\/12\/88x31.png\" data-orig-size=\"88,31\" data-comments-opened=\"1\" data-image-meta=\"{&quot;aperture&quot;:&quot;0&quot;,&quot;credit&quot;:&quot;&quot;,&quot;camera&quot;:&quot;&quot;,&quot;caption&quot;:&quot;&quot;,&quot;created_timestamp&quot;:&quot;0&quot;,&quot;copyright&quot;:&quot;&quot;,&quot;focal_length&quot;:&quot;0&quot;,&quot;iso&quot;:&quot;0&quot;,&quot;shutter_speed&quot;:&quot;0&quot;,&quot;title&quot;:&quot;&quot;,&quot;orientation&quot;:&quot;0&quot;}\" data-image-title=\"88&amp;#215;31\" data-image-description=\"\" data-image-caption=\"\" data-large-file=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2013\/12\/88x31.png\" class=\"alignright wp-image-580 size-full\" src=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2013\/12\/88x31.png\" alt=\"\" width=\"88\" height=\"31\" \/><\/a><em>&#8211; a simulator written in Mathworks Matlab for modelling the whole imaging procedure in an optical <\/em><em>fluorescence localization microscope.<\/em><\/p>\n<p><a href=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2013\/12\/testSTORM-1.png\"><img loading=\"lazy\" decoding=\"async\" data-attachment-id=\"911\" data-permalink=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/?attachment_id=911\" data-orig-file=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2013\/12\/testSTORM-1.png\" data-orig-size=\"1388,1024\" data-comments-opened=\"1\" data-image-meta=\"{&quot;aperture&quot;:&quot;0&quot;,&quot;credit&quot;:&quot;&quot;,&quot;camera&quot;:&quot;&quot;,&quot;caption&quot;:&quot;&quot;,&quot;created_timestamp&quot;:&quot;0&quot;,&quot;copyright&quot;:&quot;&quot;,&quot;focal_length&quot;:&quot;0&quot;,&quot;iso&quot;:&quot;0&quot;,&quot;shutter_speed&quot;:&quot;0&quot;,&quot;title&quot;:&quot;&quot;,&quot;orientation&quot;:&quot;0&quot;}\" data-image-title=\"testSTORM\" data-image-description=\"\" data-image-caption=\"\" data-large-file=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2013\/12\/testSTORM-1-1024x755.png\" class=\"aligncenter wp-image-911 size-large\" src=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2013\/12\/testSTORM-1-1024x755.png\" alt=\"\" width=\"530\" height=\"391\" srcset=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2013\/12\/testSTORM-1-1024x755.png 1024w, https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2013\/12\/testSTORM-1-300x221.png 300w, https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2013\/12\/testSTORM-1-768x567.png 768w, https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2013\/12\/testSTORM-1.png 1388w\" sizes=\"auto, (max-width: 530px) 100vw, 530px\" \/><\/a><\/p>\n<h3><strong>TestSTORM version 2.1.4 (2024. January) &#8211; stable<\/strong><\/h3>\n<p><strong>Matlab code: <\/strong><a style=\"outline-width: 0px !important; user-select: auto !important;\" href=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2024\/08\/testSTORM-v2.1.5.zip\">testSTORM-v2.1.5<\/a><strong><br \/>\nUser Guide: <\/strong><a href=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2018\/07\/TestSTORM_ver2.1_guide.pdf\">TestSTORM_ver2.1_guide<\/a><\/p>\n<p><strong>Release highlights:<\/strong><\/p>\n<p><a href=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2024\/08\/testSTORM-v2.1.5.zip\">v2.1.5<\/a>\u00a0(2024. August)<\/p>\n<ul>\n<li>Fixed a compatibility issue with newer Matlab versions concerning the vectorial PSF calculation.<\/li>\n<\/ul>\n<p><a href=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2024\/01\/testSTORM-v2.1.4.zip\">v2.1.4<\/a> (2024. January)<\/p>\n<ul>\n<li>Bug fix for for the dual-color simulation.<\/li>\n<li>Bug fix for the linker orientation in case of the &#8220;Disks&#8221; pattern.<\/li>\n<\/ul>\n<p><a href=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2019\/05\/testSTORM-v2.1.3.zip\">v2.1.3 <\/a>(2019. May):<\/p>\n<ul>\n<li><strong>Performance improvement<\/strong> when running the simulation with large number of labels. Significant memory reduction for the simulations (should be between 2 and 4 times).<\/li>\n<li>Axial position for the &#8220;Array&#8221; pattern now can be set in the GUI. It is useful for generating calibration files for the astigmatic 3D simulations.<\/li>\n<\/ul>\n<p><a href=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2018\/08\/testSTORM-master_v2.1.1.zip\">v2.1.1:<\/a><\/p>\n<ul>\n<li><strong>FIX<\/strong>: Fixed a bug introduced in the version 2.1 that prevented the reading of input parameters in case of using the Gaussian PSF model and resulted in an error message.<\/li>\n<li>v2.1.2 <strong>Fix<\/strong>ed a bug introduced in the version 2.1 that prevented the reading of input parameters in case of using the Gaussian PSF model and resulted in an error message.<\/li>\n<li>v2.1.2: <strong>Fix<\/strong>ed a bug affecting the &#8220;z&#8221; coordinates of the Array pattern. Now the pattern should be symmetric around the z=0 plane.<\/li>\n<li>v2.1.2: Now the PSF testing tool (&#8220;test_TestSTORM_PSF.m&#8221;) does not allow polarization sensitive simulation with the Gaussian or with the scalar PSF model.<\/li>\n<li>v2.1.2: Testing the vectorial PSF model resulted in an error message instead of the pixelized image (&#8220;and&#8221; condition should have been used instead of the &#8220;or&#8221; at two place in the code)<\/li>\n<li>v2.1.2: An error message has been added to hinder starting simulations with inconsistent Exp. time and Frame rate values.<\/li>\n<\/ul>\n<p><a href=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2018\/07\/testSTORM-v2.1.zip\">v2.1.0:<\/a><strong><br \/>\n<\/strong><\/p>\n<ul>\n<li>Replaced Matlab&#8217;s iteration to a custom one for increased reliability when calculating scalar or vectorial PSFs.<\/li>\n<li>Modification to the focal position determination when calculating scalar or vectorial PSFs. Results only slightly different focal position than the previous algorithm, in normal cases (~22 nm difference with the default settings).<\/li>\n<li>Fixed a bug when calculating scalar or vectorial PSFs (not sure whether a new Matlab version caused it or it was originally in the code). The PSFs shapes and peaks were only marginally affected.<\/li>\n<li>Made a workaround for a bug causing higher blinking event brightness when simulating with very low &#8220;Sample depth&#8221; value.<\/li>\n<li>Added &#8220;Synaptosomes&#8221; option to the random &#8220;Vesicles&#8221; pattern.<\/li>\n<li>Parameters files exported with previous TestSTORM versions (2.0.x) and containing &#8220;Rods&#8221;, &#8220;Vesicles&#8221; or &#8220;Octagons&#8221; patterns can not be imported any longer starting this version.<\/li>\n<li>Added a tool with which the generated PSF can be depicted.<br \/>\nOther clean-ups and modification in the code which should not affect the behaviour of the program.<\/li>\n<\/ul>\n<h3 style=\"text-align: left;\"><strong>TestSTORM version 2.0.4 (2018. June) &#8211; old-stable<br \/>\n<\/strong><\/h3>\n<p style=\"text-align: left;\"><strong>Matlab code<\/strong>: <a href=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2018\/06\/testSTORM-master.zip\">testSTORM-v2.0.4<\/a><br \/>\n<strong>User Guide<\/strong>: <a href=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2013\/12\/TestSTORM_ver2.0_guide.pdf\">TestSTORM_ver2.0_guide<\/a><br \/>\n<strong>Reference<\/strong>: <a href=\"https:\/\/www.nature.com\/articles\/s41598-017-01122-7\">Tibor Nov\u00e1k, Tam\u00e1s Gajdos, J\u00f3zsef Sink\u00f3, G\u00e1bor Szab\u00f3 and Mikl\u00f3s Erd\u00e9lyi: TestSTORM: Versatile simulator software for multimodal super-resolution localization fluorescence microscopy, Sci.Rep., doi: 10.1038\/s41598-017-01122-7 (2017)<\/a><br \/>\n<strong>Release highlights<\/strong>:<\/p>\n<ul>\n<li>Redesigned GUI.<\/li>\n<li style=\"text-align: left;\"><strong>New<\/strong> simulated structures: axons, npc (octagons), segmented lines and mesh<\/li>\n<li style=\"text-align: left;\"><strong>New<\/strong> PSF models: scalar (<em>Gibson and Lani<\/em>) and vectorial (<em>Richards and Wolf<\/em>)<\/li>\n<li style=\"text-align: left;\">PSF anisotropy<\/li>\n<li style=\"text-align: left;\"><strong>New<\/strong> simulation types: polarization sensitive, Dual-Colour, Astigmatic 3D<\/li>\n<li style=\"text-align: left;\">Structured background<\/li>\n<li style=\"text-align: left;\">Drift simulation<\/li>\n<li style=\"text-align: left;\">Version controlled release<\/li>\n<li><a href=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2018\/04\/testSTORM-master-63a7159d8a04fe9edfb59dd514ffd3ce9dffc550.zip\">v2.0.2<\/a>: <strong>FIX: <\/strong>stl load bugfix<\/li>\n<li><a href=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2018\/04\/testSTORM-master-63a7159d8a04fe9edfb59dd514ffd3ce9dffc550.zip\">v2.0.2<\/a>: <strong>New<\/strong> pattern upon user request<\/li>\n<li><a href=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2018\/05\/testSTORM-master.zip\">v2.0.3<\/a>: <strong>New<\/strong> disks pattern. (Cylinder shape, with labeled twin-disks inside ~130nm separated.<\/li>\n<li><a href=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2018\/05\/testSTORM-master.zip\">v2.0.3<\/a>: enabled elliptical vesicles in the GUI<\/li>\n<li><a href=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2018\/05\/testSTORM-master.zip\">v2.0.3<\/a>: <strong>FIX: <\/strong>random ves. positions, nanorod structure dye orientation, typos,<\/li>\n<li><a href=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2018\/06\/testSTORM-master.zip\">v2.0.4<\/a>: <strong>FIX: <\/strong>A serious bug was affecting the PSF size when running simulations subsequently with different parameters (e.g. wavelength).<\/li>\n<\/ul>\n<h3 style=\"text-align: left;\"><strong>TestSTORM version 1.0 (2014. Feb.) &#8211; obsolete\/EOL<br \/>\n<\/strong><\/h3>\n<p style=\"text-align: left;\"><strong>Matlab code:<\/strong><a href=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2013\/12\/testSTORM_ver1_0.zip\"> testSTORM_ver1_0.zip<\/a><br \/>\n<strong>Matlab compiled exe<\/strong>: <a href=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2013\/12\/testSTORM_ver1_0pkg.zip\">testSTORM_ver1_0pkg.zip<\/a><br \/>\n<strong>User Guide<\/strong>: <a href=\"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/wp-content\/uploads\/2015\/11\/TestSTORM_guide_ver1.pdf\">TestSTORM_guide.pdf<\/a><br \/>\n<strong>Reference<\/strong>: <a href=\"http:\/\/dx.doi.org\/10.1364\/BOE.5.000778\">Sink\u00f3, J. et. al. TestSTORM: Simulator for optimizing sample labeling and image acquisition in localization based super-resolution microscopy, Biomed. Optics Express 5, 778-787 (2014)<\/a><br \/>\n<strong>Release highlights:<\/strong><\/p>\n<ul>\n<li style=\"text-align: left;\">Initial release with Gaussian PSF and 4 simulated samples.<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>&#8211; a simulator written in Mathworks Matlab for modelling the whole imaging procedure in an optical fluorescence localization microscope. TestSTORM version 2.1.4 (2024. January) &#8211; stable Matlab code: testSTORM-v2.1.5 User<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":164,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-183","page","type-page","status-publish","hentry"],"jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/index.php?rest_route=\/wp\/v2\/pages\/183","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=183"}],"version-history":[{"count":41,"href":"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/index.php?rest_route=\/wp\/v2\/pages\/183\/revisions"}],"predecessor-version":[{"id":1908,"href":"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/index.php?rest_route=\/wp\/v2\/pages\/183\/revisions\/1908"}],"up":[{"embeddable":true,"href":"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/index.php?rest_route=\/wp\/v2\/pages\/164"}],"wp:attachment":[{"href":"https:\/\/titan.physx.u-szeged.hu\/~adoptim\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=183"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}