Install Instructions

Manual (13 MB) - note that all of the information in the manual is also available from help menus within CellProfiler.

CellProfiler Installation Guide: Macintosh OS X Version (PowerPC and Intel)

1. Download and unzip CellProfiler to any folder, but all files must remain in the same folder and the folder's name must not have spaces (e.g., /Applications/CellProfiler).

2. Download X11. Be sure to install it - usually by doubleclicking the .pkg or .dmg file. If you have trouble with this step, please ask your local tech people for help.

OS X 10.4 USERS: You must install X11 from your Tiger installation CD. The X11 provided by the Macintosh website is not supported in 10.4!

3. Copy the contents of the DMG file to your computer. To start CellProfiler, double click CellProfiler.command, located in the folder where CellProfiler was saved. The first time the program is run, it will de-compress supporting files. Due to an undiagnosed bug affecting some installations, we suggest quitting and then restarting CellProfiler.command. Then, please go to File > Set preferences and check that the Modules folder is listed correctly. If not, please browse to where you have stored the Modules folder and save these preferences.

4. (Optional steps) Get up and running quickly with one of the sample pipelines on our Examples page, and check out Help > HelpGettingStarted within CellProfiler. In CellProfiler, set some basic preferences in File > Set preferences, which will make it easier to use CellProfiler. You can drag CellProfiler.command to the dock (on the side near the trash) so the program is easily accessible in the future.

CellProfiler Installation Guide: Windows PC Version (XP and Vista)

1. Download and extract CellProfiler.exe, CellProfiler.ctf, and the Modules directory to any folder, but all files must remain in the same folder (e.g., C:\Program Files\CellProfiler).

2. Download and run the appropriate MCRInstaller for your operating system.

3. To start CellProfiler, run CellProfiler.exe. The first time the program is run, it will take a bit longer to de-compress the CTF file.

CellProfiler Installation Guide: Developer's version

1. (Mac only) Set X11 setting...

Close Matlab & X11. Open the Mac application called 'Terminal' (Applications > Utilities > Terminal)

defaults write com.apple.x11 wm_click_through -bool true

2. Start Matlab and check licenses...

Start Matlab and type into the main window (command line):

license('test','image_toolbox')

If the Image Processing Toolbox is installed with a valid license you will see ans = 1, but if ans = 0, the toolbox and/or license is not installed. CellProfiler was designed for Matlab Release 14, version 7.1, SP3 although it is possible that many functions will work on other versions. We have noticed lots of Matlab crashing with Mac OS10.2 but OS10.3 is fine.

3. Copy the CellProfiler files to your computer...

Put them in a folder named CellProfiler at any location. Suggested:

On Mac: /Applications/CellProfiler
On PC: C:\Program Files

Once the files are copied, do not move or rename this folder or any folders containing it, or you will have to repeat the next step.

4. Start CellProfiler...

To start CellProfiler for the first time, you must call it directly. After the first time, you may simply type CellProfiler in the main Matlab window to start CellProfiler. To call CellProfiler directly, type the following in the main Matlab window (LOCATION is where the CellProfiler folder is located):

On Mac: run '/LOCATION/CellProfiler/CellProfiler.m'
For example: run '/Applications/CellProfiler/CellProfiler.m'

On PC: run '\LOCATION\CellProfiler\CellProfiler.m'

For example: run 'C:\Program Files\CellProfiler\CellProfiler.m'

5. (Optional steps) Get up and running quickly with one of the sample pipelines on our Examples page, and check out Help > HelpGettingStarted within CellProfiler. In CellProfiler, set some basic preferences in File > Set preferences, which will make it easier to use CellProfiler.