Analysing Localisation Microscopy data

Starting distributed analysis infrastructure

To improve performance, PYME distributes localization analysis over multiple worker processes, with a server process used for communication. These can either all be on the same machine, or be distributed across a network/cluster. The server and worker processes need to be running before starting the analysis. This is achieved with the

launchWorkers

command. On OSX or linux, enter this in a terminal window. On Windows either enter it in an “Anaconda prompt” (found under the “Anaconda” group on the start menu, or navigate to the directory you installed Anaconda to (most likely C:\Users\<username>\Anaconda2 or C:\Users\<username>\Miniconda2) and make a shortcut to Scripts\launchWorkers.exe somewhere convenient for you.

This launchWorkers script starts the server and the same number of workers as there are cores on the current machine [1]. The server and worker processes should then find each other automatically [2] and communicate using a package called Pyro. On Windows you may be prompted to allow python through the firewall, which you should accept.

Note

We are currently in the process of migrating all our analysis to use the new, high-throughput infrastructure which is python3 compatible, faster, and more robust. This will mean that you need to run PYMEClusterOfOne (or similar), rather than launchWorkers but will leave the rest of the process largely unchanged.

Loading data

Once the server and worker processes are running, the data should be opened using dh5view.

Data acquired using PYMEAcquire

Data spooled to a .h5 file can be opened by running dh5view filename.h5, by double clicking dh5view.exe in the Anaconda\Scripts directory (or a shortcut) and using the file open dialog, or by ascociating dh5view with .h5 files. For data saved directly to a queue, the easiest way is probably to click the Analyse button on the Spooling panel in PYMEAcquire. Many protocols will do this automatically after a the intial pre-bleaching phase has been performed.

Data not acquired using PYMEAcquire

For data not originating from PYMEAcquire the process is a little more complex as dh5view will not detect that it should launch in “Localization Mode” and some metadata will probably be missing. (see Analysing data not generated by PYMEAcquire for details). In short, either use dh5view -m LM filename or use the file open dialog, complete any missing metadata entries and then choose LMAnalysis from the Modules menu.

Special attention is also needed for analysing simultaeneous multi-colour data (see Using an image splitting device for multi-colour ratiometric imaging).

With the data loaded in dh5view, one should see something like:

_images/dh5view_lm.png

Analysis settings

The Analysis and Point Finding panes in the left hand panel control the analysis settings.

Fit types

PYME offers a large number of different fit types, and is easily extensible to support more. The most useful ones are given below. If in doubt, you usually want LatGaussFitFR.

Settings

Setting Description
Threshold The threshold for event detection. This is not a strict threshold, but rather a scaling factor applied to a local threhold computed from the estimated pixel SNR. Will generally not need to be altered (except for some of the interpolation based fits)
Type The type of fit to perform
Interp The type of interpolation to perform (only methods with Interp in their name)
Start at The frame # should to start our analysis at
Background What range of frames should be used for background estimation. Uses python slice notation.
Subtract background Should we subtract the background before fitting (rather than just for event detection)
Debounce r The radius (in pixels) within which 2 events cannot be reliably distinguished
Shifts The shift field to use for chromatic shift correction (only methods with Splitter in their name.
PSF The PSF measurement to use (only Interp methods)
Track Fiducials Whether to estimate drift using fiduciaries
Variance Map An image containing a pixel by pixel map of camera variance (read noise) for sCMOS correction
Dark Map An image containing a pixel by pixel map of dark values for sCMOS correction
Flatfield Map: An image used for flatfielding (gain correction) with sCMOS cameras

Some fit modules will also display custom settings.

Starting the fitting

Testing the object detection

Whilst the threhold factor is fairly robust, it is generally worth testing the detection by clicking the Test button. This performs the object finding step on a selection of frames spaced throughout the sequence. If this fails one should check the Camera.ADOffset setting in the metadata (accessible through the Metadata tab) to see if this is reasonable before attempting to tweak the detection threshold. (The ADOffset is estimated by taking a number of dark frames before the acquisition starts, and can be fooled if the room lights are on and/or the laser shutters are misbehaving). Metadata parameters can be edited by right clicking the appropriate field in the Metadata tab.

Launching the analysis tasks

Once satisfied with the event detection, the analysis proper can be started by clicking the Go button. The results will automatically be saved as .h5r files, either under the PYMEDATADIR directory (if the environment variable was set earlier), or in a directory called PYMEData in the users home directory (c:\\Users\\<username>\\ under windows).

The resulting .h5r files can be opened in VisGUI.

Note

A crude form of distributing the analysis over multiple computers (a small ad-hoc cluster) can be achieved by:

  • Make sure that the same version of PYME is installed on all machines
  • Run launchWorkers on each machine you want to use.

A much better approach, however, is to use the ‘new-style’ distributed analysis which is both significantly faster and more robust. TODO - write docs.

Footnotes

[1]If you’re running the analysis on the data acquisition computer, and have a decent number of cores available (e.g. 8), better performance can be achieved by reserving a core for each of the Acqusition and Server processes (ie limiting the number of workers to 6 in our 8 core case). This can be done by explicitly specifying the number of workers to launch as an argument eg: launchWorkers 6.
[2]Using the zeroconf/MDNS protocol.