This is a brief introduction to troubleshooting the configuration and running a microscope via Cockpit. More detailed support can be gained by raising an issue on the Cockpit github issues page.

Startup issues

In general there are two types of startup issues, either the system does not start at all, or it begins its startup process and displays a progress window and then fails connecting to a specific device defined in the configuration files.

No response on startup

If you start Cockpit by double clicking on an icon and you receive no response after this there are few possible causes. The system may not be finding a critical component of Cockpit itself, or it may be crashing while trying to parse its configuration files as these are read before the window environment is created, and so not displayed.

The best solution to these types of problems is to start Cockpit from a command prompt instead of clicking on an icon. If the software is correctly installed you should be able to open a command prompt and type:


By starting from the command line you should get diagnostic output from Python if errors occur during startup.

If the program halts later in startup there will be windows on the screen. The “Initialising Cockpit” window contains a progress bar indicating how far the process has progressed but it also says which device is currently being initialised which is almost certainly the cause of the error.

The “Initialising Cockpit” window might be hidden by the Python errors window titled “Failed to initialise Cockpit”. This can simply be moved out of the way. This window will contain a stack of the Python code which may be beneficial in tracing obscure errors.

An additional status tool is part of Cockpit. This can be run like so:

python -m cockpit.status

This tool takes processes the Cockpit configuration files and then attempts to connect to all specified devices. The host machine is pinged to see if it is on and contactable. Then a test connection to the Pyro server of the specified device is performed. Example output from this script is below:

PING ( 56 data bytes
64 bytes from icmp_seq=0 ttl=64 time=0.053 ms

--- ping statistics ---
1 packets transmitted, 1 packets received, 0.0% packet loss
round-trip min/avg/max/stddev = 0.053/0.053/0.053/0.000 ms

DEVICE                        HOSTNAME  STATUS    PORT
======                        ========  ======    ======
Testlaser                    localhost  up        open
cameraB                      localhost  up        open
cameraG                      localhost  up        open
cameraR                      localhost  up        closed
dsp                  up        open
filterwheelB                 localhost  up        open
filterwheelG                 localhost  up        open
filterwheelR                 localhost  up        open
server               up        closed
stage                        localhost  up        open

skipped server:  in ignore list
skipped 40x:  no host or uri
skipped zPiezo:  no host or uri

In this example it can clearly be seen that cameraR is closed so is the device preventing Cockpit from starting up. This error was produced by deliberately connecting to the wrong port to generate an error on startup.

Device issues

If Cockpit started successfully then the devices defined in the depot configuration file must have been alive and able to be connected. However, most devices do not initialise the hardware until there is an enable call, generally caused by the user clicking on the control button for that device in the main window.

Most devices will be able to auto reconnect if something causes the device server process to stop. This means that generally devices can easily be reactivated by restarting the remote device server process, possibly stopping it first, and then trying to disable and re-enable the device in the Cockpit interface. The disable call will fail, generally giving a red icon next to the device name in the main window. If you then click again, Cockpit will try to reconnect to the device server and re-enable the device.

If restarting the device server and re-enabling the device in Cockpit does not work, the next step is to try and power cycle the hardware. First, stop the controlling device server and then either turn off, or disconnect the power supply. For directly powered devices such as USB cameras etc, just unplug the cable. Leave for a few seconds and reconnect power, restart the device server and attempt to reconnect from Cockpit.

If all else fails you might have the close down and restart Cockpit. This can be done either without restarting the microscope processes, or by restarting the microscope processes, effectively resetting everything.

Access to hardware triggers can be gained by opening the “debug executor” (the exact name of the menu item will be dependent on the executor name) from the Windows menu. This debug window provides toggle buttons for all digital lines as well as text boxes to control analogue outputs provided by an executor device.

Additional information about specific devices can be gained by connecting to the device from Cockpit’s own Python shell. From the Windows menu select “PyShell”. In this shell you can connect to specific devices with the code:

from cockpit import depot
device = depot.getDeviceWithName("NAME")

Where "NAME" is the device name from the Cockpit depot file. The device object then will allow access to the devices methods and values. Exactly what this can tell you is quite device dependant. This approach gives low level access to all of the devices settings and methods.

Experiment issues

Experiments are one of the most complex parts of Cockpit and issues related to running experiments can be difficult to solve.

Fundamentally, experiments involve the creation of an action table that describes what actions to take at what time. This action table is then off loaded to associated hardware, such as a DSP or the Red Pitaya single board computer, to run the actual experiment.

Experiment issues can often be diagnosed with the help of an oscilloscope, which can be used to monitor specific signals such as light or camera triggers, or analogue voltages to control Z piezo stages. Studying the existence or absence of the correct trigger pulses and their relative timing can be very helpful in diagnosing issues such as mis-synchronisation of lights and cameras.

A useful tool Cockpit provides is a graphical display of what it thinks the relevant timing signals should look like. Once an experiment has been run, the output digital and analogue signals can be displayed from the “Display last experiment” button in the “debug executor” window.

Finally it might be useful to examine the remote timing device to see what it thinks it should have performed. The Red Pitaya timing device for example, keeps a copy of all action tables uploaded.