Image Analysis Software Options for Use at Home

Supported Software (CALMN and MAGIC)

FIJI (Fiji is just image J) https://fiji.sc/ Open source (Free) software. Compatible with Window, Mac, Linux. Minimal requirement on computer specs and easy to learn. Online tutorial for self-learning: https://imagej.net/Using_Fiji

Bitplane Imaris This is an analysis software offered in the facility, which has a high requirement of computer specs. To use Imaris at home, here are a few options:

• Imaris has a basic “Viewer” that can be downloaded and used for free. There are recommended minimum system requirements, but looking at small data sets should be possible on most computers. This is a great way to look at images and share imaging with your colleagues and lab members. Click here to download the FREE Imaris Viewer and see the system recommendations.

• The CALMN and MAGIC facilities also have access to a very limited number of satellite licenses that can be accessed off site. This software can run on PC or Mac, minimum system requirements can be found here. If you have access to computer that meets the minimum requirements and would like to use one of these licenses, please contact Kaye Thomas or Yurong Gao directly. Depending on the number of requests, we will make a schedule for using the software, most likely for 2-3 days at a time.

Nikon NIS-Elements This is the software used for image acquisition on the new Nikon confocal microscope. It also has many image analysis tools. • Nikon offers free Viewer is available for both Windows and Mac systems here. • Nikon is also generously offering free temporary access to their full analysis package through May 31st. This is available for PC only and the minimum requirements can be found here. If you have access to computer that meets the minimum requirements and would like more information, please contact Kaye Thomas directly. • There is also free deconvolution you can access directly from Nikon’s website without running Elements. https://deconv.laboratory-imaging.com/process.

Olympus Fluoview This is the software used for image acquisition on the Olympus multiphoton microscope. It offers basic image visualization and 3D rendering capabilities, as well as file format change options. The software is window only. To download and use the software at home, follow the instructions below: 1. Download the software through this website: https://www.olympus- lifescience.com/en/support/downloads/#!dlOpen=%23detail847251237 2. Select the FV31S-SW Viewer under laser scanning microscopes. First register and then enter this serial number (7E90109) to be able to download. 3. To open an image, drag your images into the software.

Unsupported Software (Stuff we probably can’t help you with)

Volocity Quorum Technologies is generously offering free access to the Volocity 4D suite till April 17, 2020. This software is useful for 3D segmentation and 4D tracking. To download and use the software, details can be found on their website: https://quorumtechnologies.com/index.php/component/content/category/31- volocity-software

Amira University IT offers FEI Amira through CIRC. Amira is another image analysis software for 3D segmentation and quantifications. More information can be found on their website https://tech.rochester.edu/software/amira/

Zen Lite This is an image visualization and basic image analysis software offered by Zeiss. The software is windows only. To use the software, visit Zeiss website: https://www.zeiss.com/microscopy/us/products/microscope-software/zen-lite.html

Matlab University is now offering free Matlab license to students (an annual fee for some staff and faculties). Compatible with both Windows and Mac. If you are interested in coding your customized image analysis tools, you can download the software through University IT: https://tech.rochester.edu/news-item/matlab- now-available-free-of-charge-to-students/

You can learn matlab through the free online resources: https://www.mathworks.com/support/learn-with- matlab-tutorials.html

Leica LAS-X Leica I offering complimentary 90-day licenses for their LAS X Offline Software Suite through April 30th. This license will allow you to continue to work with your data without being physically at your microscope. https://www.leica-microsystems.com/index.php?id=28304