Quantum Detectors Merlin

LiberTEM-live supports the Merlin Medipix detectors using the TCP control and data interface.

Supported are currently 1 bit, 6 bit and 12 bit COUNTERDEPTH for both the “binary” (FILEFORMAT 0) and the “raw binary” format (FILEFORMAT 2).

For testing, an acquisition with soft trigger (TRIGGERSTART 5) is recommended since internal trigger (TRIGGERSTART 0) may cause issues with finding the beginning of the data stream. For a real STEM acquisition a hardware trigger setup that matches the given instrument is required. See the MerlinEM User Manual from Quantum Detectors for details!

Hardware and Software Requirements

You can run LiberTEM-live on the PC shipped with the Merlin detector, or you can use an external computer connected using a fast network connection (10Gbit+). Especially in a quad setup, using an external computer is recommended to keep up with the data rates at the fastest frame rates.

Usage examples

Here we briefly show how to connect to the Merlin detector system, and how to run a LiberTEM UDF on the data stream.

from libertem.viz.bqp import BQLive2DPlot
from libertem.udf.sum import SumUDF
from libertem_live.api import LiveContext, Hooks

class MyHooks(Hooks):
    def on_ready_for_data(self, env):
        """
        You can trigger the scan here, if you have a microscope control API
        """
        print("Triggering!")
        height, width = env.aq.shape.nav
        microscope.trigger_scan(width, height, dwelltime=10e-6)

ctx = LiveContext(plot_class=BQLive2DPlot)

# make a connection to the detector system:
conn = ctx.make_connection('merlin').open(
    api_host="127.0.0.1",
    api_port=MERLIN_API_PORT,
    data_host="127.0.0.1",
    data_port=MERLIN_DATA_PORT,
)

# prepare for acquisition, setting up scan parameters etc.
aq = ctx.make_acquisition(
    conn=conn,
    nav_shape=(32, 32),
    hooks=MyHooks(),
    frames_per_partition=512,
)

# run one or more UDFs on the live data stream:
ctx.run_udf(dataset=aq, udf=SumUDF())

Triggering!

Simulator

A simple simulator for testing live acquisition without the actual hardware is included in LiberTEM-live. It replays an MIB dataset and accepts the following parameters:

(libertem) $ libertem-live-mib-sim --help
Usage: libertem-live-mib-sim [OPTIONS] PATH

Options:
--nav-shape <INTEGER INTEGER>...
--continuous
--cached [NONE|MEM|MEMFD]
--host TEXT                     Address to listen on (data, control, and
                                trigger sockets)
--data-port INTEGER
--control-port INTEGER
--wait-trigger                  Wait for a SOFTTRIGGER command on the
                                control port, or a trigger signal on the
                                trigger socket
--garbage                       Send garbage before trigger. Implies --wait-
                                trigger
--max-runs INTEGER
--help                          Show this message and exit.

A suitable MIB dataset for testing can be downloaded at https://zenodo.org/record/5113449.

See the Merlin reference section for a description of the acquisition parameters.