Software

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

About using IMARIS: 

• You must reserve time with your name and cell phone number on the Imaris Outlook calendar to use this software.
• Be diligent about sticking to your reserved time slot. If you do not show up for your reserved time, the time slot will be considered open for anyone to reserve and use.
• Contact Suling to register as an Imaris user and get access to the Outlook calendar as well as be notified about Imaris learning webinars
• 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.

 
 

GIM4 Dell Precision T3610, Windows 10:

• Amira 2019, Metamorph, MatLab (available to everyone at UCSF), Microsoft Office, Image J