UCSD Baker Home Page
Introduction Lab Members Courses Images Publications Computer Programs Procedures Access Scope Facilities

  • Click on open/close to expand/contract the menu item or on the link to go directly to the page.

Transferring Images to Your Home Computer with an FTP Program

One of the easiest ways to get your image files to your home computer is to copy them first to a flash drive connected to one of the Linux computers in the EM facility. However, images can be as large as 64MB which fill up a drive fairly quickly. What is even easier is to use a FTP program. There are numerous free or "try before you buy" FTP programs available for both the Macintosh and the PC. Shown here are three such programs, Fetch, CuteFTP and FileZilla. Fetch 5.6 or higher is recommended for the Macintosh because many other FTP programs hangup after transferring certain amounts of data. You can also get a free "education license" for the program. CuteFTP is a popular program that is easy to use but it is not free. FileZilla is free and it is available for all platforms. If you are using a different program make sure you enter the same parameters mentioned below. Once a connection to the Linux machine is made your files can be dragged and dropped onto your home computer. If you are copying files to an off campus computer you might need to install the campus VPN to get access. If you are trying to get to CryoEM1 via a wireless connection make sure that you are doing this through the secure campus network.

Please remember to remove your files from the file server when you have them safely on your computer. The file server does not have unlimited storage. Old files may be removed without advance notice.


Fetch connect window This is a very popular program for the Mac OS but it is not available for the PC. When you first start the program you will get the window shown on the right. Fill in your details as shown. Make sure to choose the SFTP feature in "Connect using" and you may need to type 22 in the "Port" box. If you type the pathname as shown in the "Initial folder" window you should be able to see your folder when the connection is made. If you don't fill in the "Initial folder" box you will need to click on the Path button in the upper menu bar and then select the forward slash (/), then find the mnt folder and finally the sphera folder. Obviously, if your files are in the polara folder you will need to type that in the box instead of sphera.


When you start CuteFTP you will see the "Site Manager" window (below). You can also click on the "Site Manager" icon in the upper right area of the program window and then on the "New Site" button when the Site Manager appears.

CuteFTP connect window

Fill in the boxes as shown above. The "Label" box is just what you want to call this connection for the next time you login. Enter your username and password, type in 22 for the "Port" and choose SFTP for the "Security". Then click "Connect" at the bottom. CuteFTP is a little different than Fetch in that you have to choose the pathname where your files are with a different window. If you click View/Change Folder... you will get the window shown below. Type in the remote folder as shown in the box. Obviously, if your files are in the polara folder you will need to type that in the box instead of sphera. Your folder name can also be added at the end. You can later save this as default by clicking on Tools/Save Remote Folder as Default.
CuteFTP change folder window


FileZilla connect window
After opening FileZilla type in the "Host:" cryoem1.ucsd.edu, your username and password, and type 22 in the "Port:" window and hit "Quickconnect". In the "Remote site" type in /mnt/sphera/{yourfoldername}. You can then drag your files from the "Remote site" window to the "Local Site" window. The thing that makes this program a little more difficult to use is that the person needs to be a little bit more savvy about file systems and where files are located.
Baker Home Page Contact Site Map Search Baker Site Baker Group Calendar