{"id":29,"date":"2020-02-25T13:37:53","date_gmt":"2020-02-25T11:37:53","guid":{"rendered":"https:\/\/blogs.uef.fi\/kubiac\/?page_id=29"},"modified":"2023-12-04T13:20:39","modified_gmt":"2023-12-04T11:20:39","slug":"software","status":"publish","type":"page","link":"https:\/\/blogs.uef.fi\/kubiac\/software\/","title":{"rendered":"Open source software from KUBIAC project"},"content":{"rendered":"\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/github.com\/orukundo\/Automatic-MiniTEM-Image-Segmentation-\"> Automatic MiniTEM Image Segmentation <\/a> .&nbsp;A Software Tool for Automatic Segmentation of Adenovirus in MiniTEM Images.&nbsp;It is implemented in Matlab and its overview is presented here &#8211; <a href=\"https:\/\/www.youtube.com\/watch?v=4UZJHDPKI-g\"> in this video <\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/github.com\/AndreaBehan\/FMIS-software\">FMIS microscopy image segmentation<\/a> .&nbsp; An automated GUI-based segmentation tool to annotate cell nuclei and cell bodies in confocal microsscope images including four channels: AF647 (for goat anti-rabbit Alexa Fluor\u00ae 647), AF568 (for goat anti-mouse Alexa Fluor\u00ae 568), ZsGreen1, and DAPI.&nbsp; Implemented in Matlab , licenced under MIT license. https:\/\/github.com\/AndreaBehan\/FMIS-software<\/li>\n\n\n\n<li><a href=\"https:\/\/github.com\/AndreaBehan\/miniTEM-Image-Segmentation\">MiniTEM image segmentation<\/a> . A GUI-based tool for semi-automated annotation of MiniTEM images. Implemented in Matlab. Licensed under MIT license. https:\/\/github.com\/AndreaBehan\/miniTEM-Image-Segmentation<\/li>\n\n\n\n<li><a href=\"https:\/\/github.com\/Hierakonpolis\/MU-Net\">MU-Net-R for murine brain segmentation<\/a> . A multi-task neural network for the skull stripping and segmentation of brain MRI, implemented in PyTorch. Licensed under MIT license. https:\/\/github.com\/Hierakonpolis\/MU-Net-R.<br>Training a new network is possible with 8GB of VRAM on an NVIDIA GPU using coronal MRI slices. Higher resolution data can require up to and more than 12GB VRAM, although these requirements can be mitigated by reducing the number of kernels.<\/li>\n<\/ul>\n\n\n    <div class=\"funders grid\">\n                        <div class=\"funders__item grid__item\">\n                            <div class=\"funders__image\">\n                    <img decoding=\"async\" src=\"https:\/\/blogs.uef.fi\/kubiac\/wp-content\/uploads\/sites\/129\/2020\/02\/EU_ESR_EN_vertical_20mm_rgb.png\" alt=\"European Union, European Social Fund logo.\" \/>\n                <\/div>\n                                                <\/div>\n                        \n                        <div class=\"funders__item grid__item\">\n                            <div class=\"funders__image\">\n                    <img decoding=\"async\" src=\"https:\/\/blogs.uef.fi\/kubiac\/wp-content\/uploads\/sites\/129\/2020\/02\/leverageEU_2014_2020_rgb.png\" alt=\"Leverage from the EU 2014-2020 logo.\" \/>\n                <\/div>\n                                                <\/div>\n                        \n                        <div class=\"funders__item grid__item\">\n                            <div class=\"funders__image\">\n                    <img decoding=\"async\" src=\"https:\/\/blogs.uef.fi\/kubiac\/wp-content\/uploads\/sites\/129\/2020\/02\/ELY_yleislogo.jpg\" alt=\"Elinkeino-, liikenne- ja ymp\u00e4rist\u00f6keskuksen logo.\" \/>\n                <\/div>\n                                                <\/div>\n                        \n            <\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":329,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-29","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.3 - 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