ATFM 2016 ATFM Software installation guide

Transcription

1 ATFM 2016 Software installation guide The workshop is organized in the framework of the Czech-BioImaging research infrastructure supported by MEYS (LM ) 1

2 Software installation guide: Because the course is really hands-on and all participants are invited to have their own samples, we also expect that many participants will take their own laptops. Then, a few programs for image processing is needed. Please, read the recommendations carefully and do not hesitate to contact us directly whenever you need any assistance. Recommended Software: 1. FiJi ImageJ, up to date, SIM Check plugin included (3-6) 2. Huygens Professional deconvolution software (7-10) 3. SIM Toolbox: a MATLAB toolbox for structured illumination microscopy (11) 4. fairsim: a free, open source ImageJ/Fiji plugin for SR-SIM reconstructions (12) 5. Matlab (Trial version) (13-15) 2

3 1. FiJi ImageJ (Open source), install & update (plugin activation) FiJi allows us to open and process any raw data which we will acquire on any microscope. Moreover, the FiJi ImageJ plugin SIM Check is necessary for the SIM reconstruction analysis. Because the ImageJ needs the Java up to date, first, install/update the Java: Java update NECESSARY!!! Firs, verify whether your Java is up to date: If it is not up to date, download & install Java (e.g. for win): FiJi installation - from the link, download the FiJi version suitable for your system (Win/Mac/Linux and check weather 32 or 64bit) - move the archive file to the destination folder and extract the files. Please note, that the ProgramFiles folder is not good destination folder. DO NOT USE PROGRAM FILES as a destination folder. 3

4 FiJi update Please, read the instruction and work step-by-step open the folder Fiji.app and run the application go to Help Update.. : Click on OK: 4

5 This window appears, click on MANAGE UPDATE SITE button: Then, find and check SIM Check and click on ADD UPDATE SITE button: 5

6 After it, you can proceed with update using button APPLY CHANGES : After the Fiji restart, you should have up to date FiJi with a required plugin. 6

7 2. Huygens (Licensed, time-limited) This software we will use for STED deconvolution. Because it is licensed deconvolution software, we will provide you with the time-limited license for current (15.10) version of the software: Nevertheless, if you want to use the Huygens during the course (recommended), install the program from website. Click on download-software on the bar: Download of the software is possible after free registration: So, proceed with the registration and go to the download page. Then, select the Current Release of the software (version 15.10) according to your comp requirements: 7

8 Then, after the installation, you need to add the license. Go to Help License Overwie: 8

9 Click Add new license button: and copy the license string to the license window: HuPro wcnpsSP-x16-BftvACHMsxTuLGg2-d-2016Nov

10 Then, click Add license, OK and restart the program. The license is valid for 10 days, from Dec 3 till Dec

11 3. SIM Toolbox (a MATLAB toolbox for structured illumination microscopy) This software is an alternative tool for SIM data reconstruction. Please, download the package from the webpage: And then, follow the "Installation of the GUI (A standalone application)": 1. Download the GUI installer above. 2. Un-ZIP the file and run MyAppInstaller_web.exe. 3. MATLAB runtime is also required. If it is not already installed, it will be automatically downloaded and installed. MyAppInstaller_web.exe will guide you through the installation process. 4. We recommend following the default installation settings. 11

12 4. fairsim This software plugin for Fiji is another free available tool for SIM data reconstruction. Please, download the jar file from the webpage: and put this file into plugins folder of your Fiji installation, i.e. %Fiji installation folder%/fiji.app/plugins After restarting Fiji, fairsim menu item should be visible in Plugins. 12

13 5. MATLAB (trial version) This software will be used for a mathematical fitting of the FRAP data. The trial version of Matlab is valid for 15 days, please install it starting from e.g so that it will be valid throughout the duration of the course. To get the trial version write your address and register here as a student: 1&s_iid=hp_trial_hpg_cta2 13

14 After you verify your address, select Get packaged trial : 14

15 Then select Data Analytics and Image Processing and Computer Vision, and confirm the information. Continue your installation according to the instructions. 15

16 6. ATFM 2016 general partners Distributor of Thermo Scientific and Leica-microsystems instruments 16

17 Contact us: Course Coordinator: Ivan Novotny, PhD Light Microscopy Core Facility Institute of Molecular Genetics AS CR Videnska Praha 4 Czech Republic Phone: Fax: ivan.novotny@img.cas.cz Administration: Lenka Pišlová Microscopy Centre Institute of Molecular Genetics of the ASCR Videnska Prague 4 Czech Republic Phone: Fax: lenka.pislova@img.cas.cz 17