Software

DURING THE COVID PANDEMIC: Only one person should work in the Imaging Core room at a time. If you need to work in there it would be a good idea to check the core grant calendar to see if anyone is scheduled to work in there at the same time. Please reserve a time on the calendar if you need to work in the Imaging Core for an extended period – ideally trying to limit your reserved time to less than 4 hours at a time. Contact Suling if you need access to the calendar.

All computers have Microsoft Office, Adobe Photoshop, Adobe Illustrator, Acrobat, and ImageJ installed. Specialized software is highlighted in bold below.
 
 
GIM1 Mac Pro (Late 2013): 3.7 Ghz Quad Core Intel Xeon E5, OS 10.10.4:

•  Microsoft Office, Adobe Creative Cloud All Apps

 
 
GIM2 Dell Precision 5820, Windows 10:

• Imaris 10.0, MatLab (available to everyone at UCSF), custom-built MatLab applications – ObjectFinder and VolumeCut, Microsoft Office, Image J

About using IMARIS: 

• Register as an Imaris User: Being a registered user will give you access to notifications of training seminars. Contact Suling to register.
• Online Learning Resources: The Imaris website has a comprehensive learning center with tutorial videos, how-to articles, and webinar recordings.

Info on Custom-built MatLab apps – OBJECTFINDER and VOLUMECUT (developed by Luca Della Santina):

• ObjectFinder is a comprehensive MATLAB application package designed to automatically recognize small structures in volumetric images across large regions of the nervous system. As such, it accelerates the processing of images acquired using confocal or super-resolution microscopy from immunolabeled or fluorescent protein-expressing tissues. ObjectFinder enables shape-independent, automatic identification and co-localization of small structures such as synaptic proteins, gap junctions, neurotransmitter receptors and ion channels, allowing unprecedented scale in the quantification of distribution  and properties of such objects across large regions of the nervous system, such as an entire synaptic layer of the retina. More information, downloads and instructions for ObjectFinder are available on GitHub.
• VolumeCut is a versatile MATLAB application that allows the researcher to free-form cut an image volume without any restriction to the region that can be extracted from the image itself. It offers a substantial advantage compared to other software solutions which restrict the possibility of segmenting a volumetric region either along the three cardinal axes or along a flat but orientable plane. More information, downloads and instructions for VolumeCut are available on GitHub.
• Luca is available for 1:1 training sessions with new users that want to use the program and tailor it to their own specific data set. Email Luca.

Note: If you know in advance you need to use this computer, please reserve a time. Generally, you are welcome to use any of the computers in the room if no one is using them. But from time to time it can get get busy, so there is sign up calendar for users to reserve time on this computer. Please sign up with your name and contact info and reserve at least 1 week in advance if possible to make it easier for everyone to manage work schedules. If you do not show up for your reserved time, the time slot will be considered open for anyone to use. Contact Suling for access to the calendar.
 
 

GIM4 Dell Precision T3610, Windows 10:

• Amira 2019, Metamorph, MatLab (available to everyone at UCSF), Microsoft Office, Adobe Creative Suite CS6: Photoshop, Illustrator, Acrobat X Pro, Image J

 
 
GIM5 iMac (Late 2013): 3.1 Ghz Quad-Core Intel i7, OS 10.10.4:

• Microsoft Office 2011, Adobe Creative Suite CS6: Photoshop, Illustrator, Acrobat X Pro, Image J