{"id":299,"date":"2020-06-12T13:57:27","date_gmt":"2020-06-12T13:57:27","guid":{"rendered":"http:\/\/web.natur.cuni.cz\/IMCF\/IMCF\/?page_id=299"},"modified":"2025-06-26T13:54:05","modified_gmt":"2025-06-26T13:54:05","slug":"data-analysis-tools","status":"publish","type":"page","link":"https:\/\/imcf.natur.cuni.cz\/IMCF\/equipment\/data-analysis-tools\/","title":{"rendered":"Data analysis tools"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">Hardware:<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Offline analysis computers (OA1-5) &#8211; <em>on-site <\/em>and<em> remote access<\/em><\/li>\n\n\n\n<li>Workstations (WS1-5) with high computation power and with available leading-edge Image Analysis software (Amira, Imaris, NIS-Elements AI, Huygens) &#8211; <em>remote access only<\/em>\n<ul class=\"wp-block-list\">\n<li>WS5 is dedicated for working with LLS (Lattice light-sheet) data<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>To get access to workstations and OA computers remotely, users outside the Faculty of Science at BIOCEV need to contact Dalibor P\u00e1nek, <a href=\"mailto:dalibor.panek@natur.cuni.cz\" target=\"_blank\" rel=\"noreferrer noopener\">dalibor.panek@natur.cuni.cz<\/a>. Please, provide your BIOCEV user name for access via VPN and\/or IP address for direct access from computers at BIOCEV.<\/li>\n<\/ul>\n\n\n<div class=\"wp-block-ub-content-toggle wp-block-ub-content-toggle-block\" id=\"ub-content-toggle-block-867bfa1c-6e82-4e95-8155-42857d9bba80\" data-mobilecollapse=\"true\" data-desktopcollapse=\"true\" data-preventcollapse=\"false\" data-showonlyone=\"false\">\n<div class=\"wp-block-ub-content-toggle-accordion\" style=\"border-color: #f1f1f1; \" id=\"ub-content-toggle-panel-block-485319c9-460c-4645-8225-e2f5eaf71a1a\">\n\t\t\t<div class=\"wp-block-ub-content-toggle-accordion-title-wrap\" style=\"background-color: #f1f1f1;\" aria-controls=\"ub-content-toggle-panel-0-867bfa1c-6e82-4e95-8155-42857d9bba80\" tabindex=\"0\">\n\t\t\t<p class=\"wp-block-ub-content-toggle-accordion-title ub-content-toggle-title-867bfa1c-6e82-4e95-8155-42857d9bba80\" style=\"color: #000000; \">ACCESS CREDENTIALS TO COMPUTERS<\/p>\n\t\t\t<div class=\"wp-block-ub-content-toggle-accordion-toggle-wrap right\" style=\"color: #000000;\"><span class=\"wp-block-ub-content-toggle-accordion-state-indicator wp-block-ub-chevron-down\"><\/span><\/div>\n\t\t<\/div>\n\t\t\t<div role=\"region\" aria-expanded=\"false\" class=\"wp-block-ub-content-toggle-accordion-content-wrap ub-hide\" id=\"ub-content-toggle-panel-0-867bfa1c-6e82-4e95-8155-42857d9bba80\">\n\n<p><\/p>\n\n\n\n<table id=\"tablepress-71\" class=\"tablepress tablepress-id-71\">\n<thead>\n<tr class=\"row-1\">\n\t<th class=\"column-1\">PC<\/th><th colspan=\"3\" class=\"column-2\">Remote Desktop Connection<\/th>\n<\/tr>\n<\/thead>\n<tbody class=\"row-striping row-hover\">\n<tr class=\"row-2\">\n\t<td class=\"column-1\"><\/td><td class=\"column-2\">IP<\/td><td class=\"column-3\">Username<\/td><td class=\"column-4\">Password<\/td>\n<\/tr>\n<tr class=\"row-3\">\n\t<td class=\"column-1\">Workstation1<\/td><td class=\"column-2\">10.11.17.55<\/td><td class=\"column-3\">User Workstation 1<\/td><td class=\"column-4\">imcf<\/td>\n<\/tr>\n<tr class=\"row-4\">\n\t<td class=\"column-1\">Workstation2<\/td><td class=\"column-2\">10.11.16.23<\/td><td class=\"column-3\">ws2user<\/td><td class=\"column-4\">IMCF_2<\/td>\n<\/tr>\n<tr class=\"row-5\">\n\t<td class=\"column-1\">Workstation3<\/td><td class=\"column-2\">10.11.17.135<\/td><td class=\"column-3\">w3user<\/td><td class=\"column-4\">imcf<\/td>\n<\/tr>\n<tr class=\"row-6\">\n\t<td class=\"column-1\">Workstation5<\/td><td class=\"column-2\">10.66.75.23<\/td><td class=\"column-3\">ws5user<\/td><td class=\"column-4\">IMCF_5<\/td>\n<\/tr>\n<tr class=\"row-7\">\n\t<td class=\"column-1\">OA1<\/td><td class=\"column-2\">10.11.16.63<\/td><td class=\"column-3\">oa1user<\/td><td class=\"column-4\">imcf<\/td>\n<\/tr>\n<tr class=\"row-8\">\n\t<td class=\"column-1\">OA2<\/td><td class=\"column-2\">10.11.16.62<\/td><td class=\"column-3\">oa2user<\/td><td class=\"column-4\">imcf<\/td>\n<\/tr>\n<tr class=\"row-9\">\n\t<td class=\"column-1\">OA3<\/td><td class=\"column-2\">10.11.16.64<\/td><td class=\"column-3\">oa3user<\/td><td class=\"column-4\">imcf<\/td>\n<\/tr>\n<tr class=\"row-10\">\n\t<td class=\"column-1\">OA4<\/td><td class=\"column-2\">10.11.16.66<\/td><td class=\"column-3\">oa4user<\/td><td class=\"column-4\">imcf<\/td>\n<\/tr>\n<tr class=\"row-11\">\n\t<td class=\"column-1\">OA5<\/td><td class=\"column-2\">10.11.16.60<\/td><td class=\"column-3\">User OA5<\/td><td class=\"column-4\">imcf<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<!-- #tablepress-71 from cache -->\n\n<\/div>\n\t\t<\/div>\n\n<div class=\"wp-block-ub-content-toggle-accordion\" style=\"border-color: #f1f1f1; \" id=\"ub-content-toggle-panel-block-64974ce1-5eb3-4ae5-8142-75e4ee512d33\">\n\t\t\t<div class=\"wp-block-ub-content-toggle-accordion-title-wrap\" style=\"background-color: #f1f1f1;\" aria-controls=\"ub-content-toggle-panel-1-867bfa1c-6e82-4e95-8155-42857d9bba80\" tabindex=\"0\">\n\t\t\t<p class=\"wp-block-ub-content-toggle-accordion-title ub-content-toggle-title-867bfa1c-6e82-4e95-8155-42857d9bba80\" style=\"color: #000000; \">OVERVIEW AND TECHNICAL SPECIFICATIONS<\/p>\n\t\t\t<div class=\"wp-block-ub-content-toggle-accordion-toggle-wrap right\" style=\"color: #000000;\"><span class=\"wp-block-ub-content-toggle-accordion-state-indicator wp-block-ub-chevron-down\"><\/span><\/div>\n\t\t<\/div>\n\t\t\t<div role=\"region\" aria-expanded=\"false\" class=\"wp-block-ub-content-toggle-accordion-content-wrap ub-hide\" id=\"ub-content-toggle-panel-1-867bfa1c-6e82-4e95-8155-42857d9bba80\">\n\n<p><\/p>\n\n\n\n<table id=\"tablepress-72\" class=\"tablepress tablepress-id-72\">\n<thead>\n<tr class=\"row-1\">\n\t<th class=\"column-1\">PC<\/th><th class=\"column-2\">CPU<\/th><th class=\"column-3\">GPU<\/th><th class=\"column-4\">RAM<\/th><th class=\"column-5\">Room<\/th><th class=\"column-6\">Add-ons<\/th>\n<\/tr>\n<\/thead>\n<tbody class=\"row-striping row-hover\">\n<tr class=\"row-2\">\n\t<td class=\"column-1\">Workstation1<\/td><td class=\"column-2\">Intel Xeon W-2145<br \/>\n3.70GHz, 8 cores<\/td><td class=\"column-3\">NVIDIA Quadro RTX 5000<\/td><td class=\"column-4\">128GB<\/td><td class=\"column-5\">remote access only<\/td><td class=\"column-6\"><\/td>\n<\/tr>\n<tr class=\"row-3\">\n\t<td class=\"column-1\">Workstation2<\/td><td class=\"column-2\">AMD EPYC 7302 <br \/>\n3.0 GHz, 16 cores<\/td><td class=\"column-3\">NVIDIA GeForce RTX 3090<\/td><td class=\"column-4\">128GB<\/td><td class=\"column-5\">remote access only<\/td><td class=\"column-6\"><\/td>\n<\/tr>\n<tr class=\"row-4\">\n\t<td class=\"column-1\">Workstation3<\/td><td class=\"column-2\">AMD EPYC 7302<br \/>\n3.0 GHz, 16 cores<\/td><td class=\"column-3\">NVIDIA GeForce RTX 3090<\/td><td class=\"column-4\">128GB<\/td><td class=\"column-5\">remote access only<\/td><td class=\"column-6\"><\/td>\n<\/tr>\n<tr class=\"row-5\">\n\t<td class=\"column-1\">Workstation4<\/td><td class=\"column-2\">AMD EPYC 7302<br \/>\n3.0 GHz, 16 cores<\/td><td class=\"column-3\">4x NVIDIA GeForce RTX 3090<\/td><td class=\"column-4\">128GB<\/td><td class=\"column-5\">remote access only<\/td><td class=\"column-6\"><\/td>\n<\/tr>\n<tr class=\"row-6\">\n\t<td class=\"column-1\">Workstation5<\/td><td class=\"column-2\">AMD EPYC 9124<br \/>\n3.0 GHz, 16 cores<\/td><td class=\"column-3\">2x NVIDIA RTX A6000<\/td><td class=\"column-4\">512GB<\/td><td class=\"column-5\">remote access only<\/td><td class=\"column-6\"><\/td>\n<\/tr>\n<tr class=\"row-7\">\n\t<td class=\"column-1\">OA1<\/td><td class=\"column-2\">Intel Core i5-13500<br \/>\n2.5 GHz, 14 cores<\/td><td class=\"column-3\">NVIDIA GeForce GTX 1650 4GB<\/td><td class=\"column-4\">32GB<\/td><td class=\"column-5\">BIOCEV L1.005<\/td><td class=\"column-6\"><\/td>\n<\/tr>\n<tr class=\"row-8\">\n\t<td class=\"column-1\">OA2<\/td><td class=\"column-2\">AMD Ryzen 9 5900X<br \/>\n3.70 GHz, 12 cores <\/td><td class=\"column-3\">NVIDIA GeForce RTF 4060 Ti<\/td><td class=\"column-4\">32GB<\/td><td class=\"column-5\">BIOCEV L1.005<\/td><td class=\"column-6\">Touch screen and pen<\/td>\n<\/tr>\n<tr class=\"row-9\">\n\t<td class=\"column-1\">OA3<\/td><td class=\"column-2\">AMD Ryzen 9 5900X<br \/>\n3.70 GHz, 12 cores <\/td><td class=\"column-3\">NVIDIA GeForce RTF 4060 Ti<\/td><td class=\"column-4\">32GB<\/td><td class=\"column-5\">BIOCEV L1.005<\/td><td class=\"column-6\"><\/td>\n<\/tr>\n<tr class=\"row-10\">\n\t<td class=\"column-1\">OA4<\/td><td class=\"column-2\">Intel Core i5-13500<br \/>\n2.5 GHz, 14 cores<\/td><td class=\"column-3\">NVIDIA GeForce GTX 1650 4GB<\/td><td class=\"column-4\">32GB<\/td><td class=\"column-5\">BIOCEV L1.005<\/td><td class=\"column-6\"><\/td>\n<\/tr>\n<tr class=\"row-11\">\n\t<td class=\"column-1\">OA5<\/td><td class=\"column-2\">Intel Core i7-4790 <br \/>\n3.0 GHz, 4 cores<\/td><td class=\"column-3\">AMD Radeon R7 200<\/td><td class=\"column-4\">16GB<\/td><td class=\"column-5\">BIOCEV L1.005<\/td><td class=\"column-6\"><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<!-- #tablepress-72 from cache -->\n\n<\/div>\n\t\t<\/div>\n<\/div>\n\n\n<div style=\"height:50px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h2 class=\"wp-block-heading\">Software:<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li>When using software with limited number of licences on dedicated IMCF computer, <strong>reservation of both software license and PC is required<\/strong>.<\/li>\n<\/ul>\n\n\n<div class=\"wp-block-ub-content-toggle wp-block-ub-content-toggle-block\" id=\"ub-content-toggle-block-def999b4-84b4-4165-b966-c99e7711764c\" data-mobilecollapse=\"true\" data-desktopcollapse=\"true\" data-preventcollapse=\"false\" data-showonlyone=\"false\">\n<div class=\"wp-block-ub-content-toggle-accordion\" style=\"border-color: #f1f1f1; \" id=\"ub-content-toggle-panel-block-a4fce988-4883-4bf4-9660-2550d871a6fd\">\n\t\t\t<div class=\"wp-block-ub-content-toggle-accordion-title-wrap\" style=\"background-color: #f1f1f1;\" aria-controls=\"ub-content-toggle-panel-0-def999b4-84b4-4165-b966-c99e7711764c\" tabindex=\"0\">\n\t\t\t<p class=\"wp-block-ub-content-toggle-accordion-title ub-content-toggle-title-def999b4-84b4-4165-b966-c99e7711764c\" style=\"color: #000000; \">SOFTWARE OVERVIEW<\/p>\n\t\t\t<div class=\"wp-block-ub-content-toggle-accordion-toggle-wrap right\" style=\"color: #000000;\"><span class=\"wp-block-ub-content-toggle-accordion-state-indicator wp-block-ub-chevron-down\"><\/span><\/div>\n\t\t<\/div>\n\t\t\t<div role=\"region\" aria-expanded=\"false\" class=\"wp-block-ub-content-toggle-accordion-content-wrap ub-hide\" id=\"ub-content-toggle-panel-0-def999b4-84b4-4165-b966-c99e7711764c\">\n\n<p><\/p>\n\n\n\n<table id=\"tablepress-3\" class=\"tablepress tablepress-id-3 tbody-has-connected-cells\">\n<tbody class=\"row-striping row-hover\">\n<tr class=\"row-1\">\n\t<td colspan=\"2\" class=\"column-1\"><h3>Commercial software<\/h3><\/td>\n<\/tr>\n<tr class=\"row-2\">\n\t<td class=\"column-1\">Amira<br \/>\n2024.1<\/td><td class=\"column-2\"><ul><li>1 floating license available on Workstation1, Workstation2, OA1, OA2, OA4<br \/>\n<\/li><li>charged per hour - see <a rel=\"noreferrer noopener\" href=\"https:\/\/imcf.natur.cuni.cz\/IMCF\/price-lists\/\" target=\"_blank\">Price list <\/a><br \/>\n<\/li><li><a rel=\"noreferrer noopener\" href=\"http:\/\/imcf.natur.cuni.cz\/IMCF\/wp-content\/uploads\/2022\/01\/Amira_Navod_1.pdf\" target=\"_blank\">manual for remote access [PDF]<\/a><\/li><\/ul><br \/>\n<\/li><li> Version history: 2023.1 > 9.9.2024, 2022.2 > 1.9.2023<\/td>\n<\/tr>\n<tr class=\"row-3\">\n\t<td class=\"column-1\">Imaris<br \/>\n9.9.1<\/td><td class=\"column-2\"><ul><li>1 floating license \u2013> available on Workstation1, Workstation2, OA2<br \/>\n<\/li><li><a rel=\"noreferrer noopener\" href=\"http:\/\/imcf.natur.cuni.cz\/IMCF\/wp-content\/uploads\/2022\/10\/Imaris_Manual.pdf\" target=\"_blank\">manual for remote access [PDF]<\/a><\/li><\/ul><\/td>\n<\/tr>\n<tr class=\"row-4\">\n\t<td class=\"column-1\">Kaluza<\/td><td class=\"column-2\"><ul><li>10 floating licenses available for your personal PCs, available as well on OA5 PC <br \/>\n<\/li><li>personal PCs preferred \u2013 users using FlowJo are therefore not blocked<br \/>\n<\/li><li><a rel=\"noreferrer noopener\" href=\"http:\/\/imcf.natur.cuni.cz\/IMCF\/wp-content\/uploads\/2020\/06\/Kaluza-remote-access.pdf\" target=\"_blank\">manual for remote access [PDF]<\/a><\/li><\/ul><\/td>\n<\/tr>\n<tr class=\"row-5\">\n\t<td class=\"column-1\">FlowJo<\/td><td class=\"column-2\"><ul><li>1 license available on OA5 PC<br \/>\n<\/li><li><a rel=\"noreferrer noopener\" href=\"http:\/\/imcf.natur.cuni.cz\/IMCF\/wp-content\/uploads\/2023\/04\/FlowJo-FROM-YOUR-COMPUTER-USING-OA5-LICENSE.pdf\" target=\"_blank\">manual for remote access [PDF]<\/a><\/li><\/ul><br \/>\n<ul><li>1 license available directly from personal PC<br \/>\n<\/li><li><a rel=\"noreferrer noopener\" href=\"http:\/\/imcf.natur.cuni.cz\/IMCF\/wp-content\/uploads\/2023\/04\/FlowJo-FROM-YOUR-COMPUTER-USING-FLOATING-LICENSE.pdf\" target=\"_blank\">manual for remote access [PDF]<\/a><\/li><\/ul><\/td>\n<\/tr>\n<tr class=\"row-6\">\n\t<td class=\"column-1\">Huygens Professional<br \/>\n25.04<\/td><td class=\"column-2\"><ul><li>2 licenses can be used at the same time <br \/>\n<\/li><li>pre-installed on Workstations 1, 2, 3, 5 and OA1-4 PCs<br \/>\n<\/li><li>charged per hour - see <a rel=\"noreferrer noopener\" href=\"https:\/\/imcf.natur.cuni.cz\/IMCF\/price-lists\/\" target=\"_blank\">Price list<\/a><br \/>\n<\/li><li>for manual to access Huygens refer to <a rel=\"noreferrer noopener\" href=\"http:\/\/imcf.natur.cuni.cz\/IMCF\/wp-content\/uploads\/2025\/07\/Huygens-guide.pdf\" target=\"_blank\">Huygens manual [PDF]<\/a><br \/>\n<\/li><\/td>\n<\/tr>\n<tr class=\"row-7\">\n\t<td class=\"column-1\">NIS-Elements (with AI)<br \/>\n6.0.2<\/td><td class=\"column-2\"><ul><li>2 licenses can be used at the same time <br \/>\n<\/li><li>pre-installed on Workstation1, Workstation2, OA1-4 PCs<br \/>\n<\/li><li>for remote access to our workstations refer to <a rel=\"noreferrer noopener\" href=\"http:\/\/imcf.natur.cuni.cz\/IMCF\/wp-content\/uploads\/2020\/06\/Remote-Access.pdf\" target=\"_blank\">general manual [PDF]<\/a><br \/>\n<\/td>\n<\/tr>\n<tr class=\"row-8\">\n\t<td class=\"column-1\">Matlab<\/td><td class=\"column-2\"><ul><li>available on OA1-4 PCs and Workstation1<br \/>\n<\/li><li>all toolboxes are available, just contact member of IMCF for upgrade<br \/>\n<\/li><li>for remote access refer to <a rel=\"noreferrer noopener\" href=\"http:\/\/imcf.natur.cuni.cz\/IMCF\/wp-content\/uploads\/2020\/06\/Remote-Access.pdf\" target=\"_blank\">general manual [PDF]<\/a><\/li><\/ul><\/td>\n<\/tr>\n<tr class=\"row-9\">\n\t<td class=\"column-1\">LabVIEW<\/td><td class=\"column-2\"><ul><li>home-made tools \u201cTTTR Data Analysis\u201d and \u201cData analysis_18\u201d for FLIM and point and line-scan FCS data analysis<br \/>\n<\/li><li>available on OA3 PC<br \/>\n<\/li><li>for remote access refer to <a rel=\"noreferrer noopener\" href=\"http:\/\/imcf.natur.cuni.cz\/IMCF\/wp-content\/uploads\/2020\/06\/Remote-Access.pdf\" target=\"_blank\">general manual [PDF]<\/a><\/li><\/ul><\/td>\n<\/tr>\n<tr class=\"row-10\">\n\t<td colspan=\"2\" class=\"column-1\"><h3>Installed freeware tools<\/h3><\/td>\n<\/tr>\n<tr class=\"row-11\">\n\t<td class=\"column-1\">FIJI<\/td><td class=\"column-2\"><ul><li>available on OA1-4, Workstation1-3, and most microscopic computers<\/li><\/ul><\/td>\n<\/tr>\n<tr class=\"row-12\">\n\t<td class=\"column-1\">QuPath<\/td><td class=\"column-2\"><ul><li>available on Workstation 1 and 2<\/li><\/ul><\/td>\n<\/tr>\n<tr class=\"row-13\">\n\t<td class=\"column-1\">Python, Napari, R<\/td><td class=\"column-2\"><ul><li>on request<\/li><\/ul><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<!-- #tablepress-3 from cache -->\n\n<\/div>\n\t\t<\/div>\n\n<div class=\"wp-block-ub-content-toggle-accordion\" style=\"border-color: #f1f1f1; \" id=\"ub-content-toggle-panel-block-a377e990-88ba-4139-aa77-26707f0c0c81\">\n\t\t\t<div class=\"wp-block-ub-content-toggle-accordion-title-wrap\" style=\"background-color: #f1f1f1;\" aria-controls=\"ub-content-toggle-panel-1-def999b4-84b4-4165-b966-c99e7711764c\" tabindex=\"0\">\n\t\t\t<p class=\"wp-block-ub-content-toggle-accordion-title ub-content-toggle-title-def999b4-84b4-4165-b966-c99e7711764c\" style=\"color: #000000; \">SOFTWARE AVAILABILITY ON IMCF COMPUTERS<\/p>\n\t\t\t<div class=\"wp-block-ub-content-toggle-accordion-toggle-wrap right\" style=\"color: #000000;\"><span class=\"wp-block-ub-content-toggle-accordion-state-indicator wp-block-ub-chevron-down\"><\/span><\/div>\n\t\t<\/div>\n\t\t\t<div role=\"region\" aria-expanded=\"false\" class=\"wp-block-ub-content-toggle-accordion-content-wrap ub-hide\" id=\"ub-content-toggle-panel-1-def999b4-84b4-4165-b966-c99e7711764c\">\n\n<p><\/p>\n\n\n\n<table id=\"tablepress-52\" class=\"tablepress tablepress-id-52\">\n<tbody class=\"row-striping row-hover\">\n<tr class=\"row-1\">\n\t<td class=\"column-1\"><\/td><td class=\"column-2\">OA1<\/td><td class=\"column-3\">OA2<\/td><td class=\"column-4\">OA3<\/td><td class=\"column-5\">OA4<\/td><td class=\"column-6\">OA5<\/td><td class=\"column-7\">Workstation 1<\/td><td class=\"column-8\">Workstation 2<\/td><td class=\"column-9\">Workstation 3<\/td><td class=\"column-10\">Workstation 5<\/td>\n<\/tr>\n<tr class=\"row-2\">\n\t<td class=\"column-1\">Amira<\/td><td class=\"column-2\">\u2714<\/td><td class=\"column-3\">\u2714<\/td><td class=\"column-4\"><\/td><td class=\"column-5\">\u2714<\/td><td class=\"column-6\"><\/td><td class=\"column-7\">\u2714<\/td><td class=\"column-8\">\u2714<\/td><td class=\"column-9\"><\/td><td class=\"column-10\"><\/td>\n<\/tr>\n<tr class=\"row-3\">\n\t<td class=\"column-1\">Imaris<\/td><td class=\"column-2\"><\/td><td class=\"column-3\">\u2714<\/td><td class=\"column-4\"><\/td><td class=\"column-5\"><\/td><td class=\"column-6\"><\/td><td class=\"column-7\">\u2714<\/td><td class=\"column-8\">\u2714<\/td><td class=\"column-9\"><\/td><td class=\"column-10\">\u2714<\/td>\n<\/tr>\n<tr class=\"row-4\">\n\t<td class=\"column-1\">NIS-Elements<\/td><td class=\"column-2\">\u2714<\/td><td class=\"column-3\">\u2714<\/td><td class=\"column-4\">\u2714<\/td><td class=\"column-5\">\u2714<\/td><td class=\"column-6\"><\/td><td class=\"column-7\">\u2714<\/td><td class=\"column-8\">\u2714<\/td><td class=\"column-9\"><\/td><td class=\"column-10\">\u2714<\/td>\n<\/tr>\n<tr class=\"row-5\">\n\t<td class=\"column-1\">Huygens<\/td><td class=\"column-2\">\u2714<\/td><td class=\"column-3\">\u2714<\/td><td class=\"column-4\">\u2714<\/td><td class=\"column-5\">\u2714<\/td><td class=\"column-6\"><\/td><td class=\"column-7\">\u2714<\/td><td class=\"column-8\">\u2714<\/td><td class=\"column-9\">\u2714<\/td><td class=\"column-10\">\u2714<\/td>\n<\/tr>\n<tr class=\"row-6\">\n\t<td class=\"column-1\">LabVIEW<\/td><td class=\"column-2\"><\/td><td class=\"column-3\"><\/td><td class=\"column-4\">\u2714<\/td><td class=\"column-5\"><\/td><td class=\"column-6\"><\/td><td class=\"column-7\"><\/td><td class=\"column-8\"><\/td><td class=\"column-9\"><\/td><td class=\"column-10\"><\/td>\n<\/tr>\n<tr class=\"row-7\">\n\t<td class=\"column-1\">Matlab<\/td><td class=\"column-2\">\u2714<\/td><td class=\"column-3\">\u2714<\/td><td class=\"column-4\">\u2714<\/td><td class=\"column-5\">\u2714<\/td><td class=\"column-6\"><\/td><td class=\"column-7\">\u2714<\/td><td class=\"column-8\"><\/td><td class=\"column-9\"><\/td><td class=\"column-10\"><\/td>\n<\/tr>\n<tr class=\"row-8\">\n\t<td class=\"column-1\">FIJI<\/td><td class=\"column-2\">\u2714<\/td><td class=\"column-3\">\u2714<\/td><td class=\"column-4\">\u2714<\/td><td class=\"column-5\">\u2714<\/td><td class=\"column-6\"><\/td><td class=\"column-7\">\u2714<\/td><td class=\"column-8\">\u2714<\/td><td class=\"column-9\">\u2714<\/td><td class=\"column-10\">\u2714<\/td>\n<\/tr>\n<tr class=\"row-9\">\n\t<td class=\"column-1\">QuPath<\/td><td class=\"column-2\"><\/td><td class=\"column-3\"><\/td><td class=\"column-4\"><\/td><td class=\"column-5\"><\/td><td class=\"column-6\"><\/td><td class=\"column-7\">\u2714<\/td><td class=\"column-8\">\u2714<\/td><td class=\"column-9\"><\/td><td class=\"column-10\">\u2714<\/td>\n<\/tr>\n<tr class=\"row-10\">\n\t<td class=\"column-1\">Lightbox &amp; Imspector<\/td><td class=\"column-2\">\u2714<\/td><td class=\"column-3\"><\/td><td class=\"column-4\">\u2714<\/td><td class=\"column-5\"><\/td><td class=\"column-6\"><\/td><td class=\"column-7\">\u2714<\/td><td class=\"column-8\"><\/td><td class=\"column-9\"><\/td><td class=\"column-10\"><\/td>\n<\/tr>\n<tr class=\"row-11\">\n\t<td class=\"column-1\">Kaluza<\/td><td class=\"column-2\"><\/td><td class=\"column-3\"><\/td><td class=\"column-4\"><\/td><td class=\"column-5\"><\/td><td class=\"column-6\">\u2714<\/td><td class=\"column-7\"><\/td><td class=\"column-8\"><\/td><td class=\"column-9\"><\/td><td class=\"column-10\"><\/td>\n<\/tr>\n<tr class=\"row-12\">\n\t<td class=\"column-1\">FlowJo<\/td><td class=\"column-2\"><\/td><td class=\"column-3\"><\/td><td class=\"column-4\"><\/td><td class=\"column-5\"><\/td><td class=\"column-6\">\u2714<\/td><td class=\"column-7\"><\/td><td class=\"column-8\"><\/td><td class=\"column-9\"><\/td><td class=\"column-10\"><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<!-- #tablepress-52 from cache -->\n\n<\/div>\n\t\t<\/div>\n<\/div>\n\n\n<div style=\"height:50px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h2 class=\"wp-block-heading\">Data management (OMERO):<\/h2>\n\n\n\n<p>OMERO (Open Microscopy Environment) is a powerful platform designed to facilitate the management, sharing, and analysis of microscopy data. Researchers can access OMERO at IMCF through a web interface at <a href=\"https:\/\/www.openmicroscopy.org\/omero\/\"><\/a><a rel=\"noreferrer noopener\" href=\"http:\/\/omero.natur.biocev.org\/\" target=\"_blank\">omero.natur.biocev.org<\/a>, making it easy to view and analyze their datasets remotely.<\/p>\n\n\n\n<p>OMERO aligns with the FAIR principles, which stand for Findable, Accessible, Interoperable, and Reusable. By adhering to these principles, OMERO ensures that microscopy data becomes more discoverable and accessible, fostering data sharing and reusability across research communities. The FAIR principles promote open science and contribute to the integrity and transparency of research.<\/p>\n\n\n<div class=\"wp-block-ub-content-toggle wp-block-ub-content-toggle-block\" id=\"ub-content-toggle-block-81f52298-7add-48d1-87c3-3903621fafd2\" data-mobilecollapse=\"true\" data-desktopcollapse=\"true\" data-preventcollapse=\"false\" data-showonlyone=\"false\">\n<div class=\"wp-block-ub-content-toggle-accordion\" style=\"border-color: #f1f1f1; \" id=\"ub-content-toggle-panel-block-7a9083a7-7fc3-48bc-af38-fb8264dcd16a\">\n\t\t\t<div class=\"wp-block-ub-content-toggle-accordion-title-wrap\" style=\"background-color: #f1f1f1;\" aria-controls=\"ub-content-toggle-panel-0-81f52298-7add-48d1-87c3-3903621fafd2\" tabindex=\"0\">\n\t\t\t<p class=\"wp-block-ub-content-toggle-accordion-title ub-content-toggle-title-81f52298-7add-48d1-87c3-3903621fafd2\" style=\"color: #000000; \">GET ACCESS<\/p>\n\t\t\t<div class=\"wp-block-ub-content-toggle-accordion-toggle-wrap right\" style=\"color: #000000;\"><span class=\"wp-block-ub-content-toggle-accordion-state-indicator wp-block-ub-chevron-down\"><\/span><\/div>\n\t\t<\/div>\n\t\t\t<div role=\"region\" aria-expanded=\"false\" class=\"wp-block-ub-content-toggle-accordion-content-wrap ub-hide\" id=\"ub-content-toggle-panel-0-81f52298-7add-48d1-87c3-3903621fafd2\">\n\n<p>For access to OMERO, users must have a valid BIOCEV account.<\/p>\n\n\n\n<ol class=\"wp-block-list\">\n<li>Request an access to OMERO from IMCF staff and wait for confirmation.<\/li>\n<\/ol>\n\n\n\n<ol start=\"2\" class=\"wp-block-list\">\n<li>Log in at <a href=\"http:\/\/omero.natur.biocev.org\" data-type=\"URL\" data-id=\"omero.natur.biocev.org\" target=\"_blank\" rel=\"noreferrer noopener\">omero.natur.biocev.org<\/a> with your BIOCEV credentials.<\/li>\n<\/ol>\n\n\n\n<ol start=\"3\" class=\"wp-block-list\">\n<li>If successfully logged in, an account has been created for you. You should see something like this (with your name instead)<\/li>\n<\/ol>\n\n\n\n<figure class=\"wp-block-image size-full is-resized\"><img loading=\"lazy\" decoding=\"async\" width=\"565\" height=\"346\" src=\"https:\/\/imcf.natur.cuni.cz\/IMCF\/wp-content\/uploads\/2023\/07\/image-4.png\" alt=\"\" class=\"wp-image-2209\" style=\"width:494px;height:302px\" srcset=\"https:\/\/imcf.natur.cuni.cz\/IMCF\/wp-content\/uploads\/2023\/07\/image-4.png 565w, https:\/\/imcf.natur.cuni.cz\/IMCF\/wp-content\/uploads\/2023\/07\/image-4-300x184.png 300w, https:\/\/imcf.natur.cuni.cz\/IMCF\/wp-content\/uploads\/2023\/07\/image-4-490x300.png 490w\" sizes=\"auto, (max-width: 565px) 100vw, 565px\" \/><\/figure>\n\n\n\n<ol start=\"4\" class=\"wp-block-list\">\n<li>Let the IMCF staff know that you successfully logged in and your account will be linked with relevant data repositories.<\/li>\n<\/ol>\n\n\n\n<ol start=\"5\" class=\"wp-block-list\">\n<li>When linked, you can access shared data by clicking on the panel <em>users \u2018yourname\u2019<\/em>. List of groups you have been granted access to will be shown. To show data, choose <em>All Members<\/em> from the associated group.<\/li>\n<\/ol>\n\n\n\n<figure class=\"wp-block-image size-full is-resized\"><img loading=\"lazy\" decoding=\"async\" width=\"692\" height=\"332\" src=\"https:\/\/imcf.natur.cuni.cz\/IMCF\/wp-content\/uploads\/2023\/07\/image-5.png\" alt=\"\" class=\"wp-image-2210\" style=\"width:495px;height:236px\" srcset=\"https:\/\/imcf.natur.cuni.cz\/IMCF\/wp-content\/uploads\/2023\/07\/image-5.png 692w, https:\/\/imcf.natur.cuni.cz\/IMCF\/wp-content\/uploads\/2023\/07\/image-5-300x144.png 300w, https:\/\/imcf.natur.cuni.cz\/IMCF\/wp-content\/uploads\/2023\/07\/image-5-500x240.png 500w\" sizes=\"auto, (max-width: 692px) 100vw, 692px\" \/><\/figure>\n\n\n\n<ol start=\"6\" class=\"wp-block-list\">\n<li>Images are to be found inside Project (grey) and Dataset (green) folders.<\/li>\n<\/ol>\n\n\n\n<figure class=\"wp-block-image size-full is-resized\"><img loading=\"lazy\" decoding=\"async\" width=\"697\" height=\"351\" src=\"https:\/\/imcf.natur.cuni.cz\/IMCF\/wp-content\/uploads\/2023\/07\/image-3.png\" alt=\"\" class=\"wp-image-2208\" style=\"width:497px;height:250px\" srcset=\"https:\/\/imcf.natur.cuni.cz\/IMCF\/wp-content\/uploads\/2023\/07\/image-3.png 697w, https:\/\/imcf.natur.cuni.cz\/IMCF\/wp-content\/uploads\/2023\/07\/image-3-300x151.png 300w, https:\/\/imcf.natur.cuni.cz\/IMCF\/wp-content\/uploads\/2023\/07\/image-3-500x252.png 500w\" sizes=\"auto, (max-width: 697px) 100vw, 697px\" \/><\/figure>\n\n<\/div>\n\t\t<\/div>\n<\/div>","protected":false},"excerpt":{"rendered":"<p>Hardware: Software: Data management (OMERO): OMERO (Open Microscopy Environment) is a powerful platform designed to facilitate the management, sharing, and analysis of microscopy data. Researchers can access OMERO at IMCF through a web interface at omero.natur.biocev.org, making it easy to &hellip; <a href=\"https:\/\/imcf.natur.cuni.cz\/IMCF\/equipment\/data-analysis-tools\/\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":181,"menu_order":4,"comment_status":"closed","ping_status":"closed","template":"sidebar-page.php","meta":{"ngg_post_thumbnail":0,"footnotes":""},"class_list":["post-299","page","type-page","status-publish","hentry"],"featured_image_src":null,"_links":{"self":[{"href":"https:\/\/imcf.natur.cuni.cz\/IMCF\/wp-json\/wp\/v2\/pages\/299","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/imcf.natur.cuni.cz\/IMCF\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/imcf.natur.cuni.cz\/IMCF\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/imcf.natur.cuni.cz\/IMCF\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/imcf.natur.cuni.cz\/IMCF\/wp-json\/wp\/v2\/comments?post=299"}],"version-history":[{"count":24,"href":"https:\/\/imcf.natur.cuni.cz\/IMCF\/wp-json\/wp\/v2\/pages\/299\/revisions"}],"predecessor-version":[{"id":2912,"href":"https:\/\/imcf.natur.cuni.cz\/IMCF\/wp-json\/wp\/v2\/pages\/299\/revisions\/2912"}],"up":[{"embeddable":true,"href":"https:\/\/imcf.natur.cuni.cz\/IMCF\/wp-json\/wp\/v2\/pages\/181"}],"wp:attachment":[{"href":"https:\/\/imcf.natur.cuni.cz\/IMCF\/wp-json\/wp\/v2\/media?parent=299"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}