FLIMfit software for FLIM data analysis

Our FLIMfit software is describe in Warren et al, PLoS ONE 8 (2013) e70687.  Please cite this paper if you use the FLIMfit software.

The FLIMfit software package is written in MATLAB and is available as a client for the OMERO platform and can also be used as a stand-alone MATLAB application. It is available at https://flimfit.org/

FLIM of fluorescent proteins.

Our MATLAB software tool for correcting fluorescence lifetime values of fluorescent proteins determined without taking account of the static distribution of fluorophore dipoles (Alexandrov et al, J Biophotonics, 11 (2018) e201700366) can be downloaded at https://github.com/yalexand/dk2_to_sk2_calculator

openFLIM-GOI software for wide-field time-gated FLIM

Our openFLIM-GOI software for instrument control and data acquisition using wide-field time-gated imaging is written in MicroManager and is available at https://github.com/imperial-photonics/openFLIM-GOI

openFLIM-HCA software for automated multiwell plate wide-field time-gated FLIM

Our openFLIM-HCA software for automated instrument control and data acquisition using wide-field time-gated FLIM of samples arrayed in a 96 well plate is written in MicroManager and is available at https://github.com/imperial-photonics/openFLIM-HCA/wiki

Analysis of openFLIM HCA data can be undertaken using FLIMfit


Optical projection tomography (OPT)

Our OPT software software for OPT data acquisition written in MicroManager can be downloaded here

OPT data can be reconstructed using Radon_Transform.jar, an open source Radon Transform plug-in written by Damien Farrell for ImageJ. Instructions are available for download

Our machine-learning based software for removing streak artefacts when reconstructing sparse OPT data sets (Davis et al, J Biophotonics, 112 (2019) e201900128) can be downloaded at https://github.com/imperial-photonics/CNOPT


Single molecule localisation microscopy

We typically acquire easySTORM image data using the MicroManager Multidimensional Acquisition (MDA) plugin. We typically also run our openFocus plugin for MicroManager in focus-lock mode. 

HPC processing of SMLM data: the scripts that we run on our HPC cluster for the work presented here can be accessed at: https://github.com/ImperialCollegeLondon/HPC_STORM


openFocus - an open source autofocus hardware module

When using a microscope equipped with an implementation of the openFocus hardware, our MicroManager openFocus plugin can be run in parallel with the Multidimensional Acquisition (MDA) plugin. We typically it in focus-lock mode for, e.g., easySTORM. However, it can also provide long z-range operation in single-shot mode, which can be useful when moving between "distant" fields of view, e.g. across multiwell plates. 

The openFocus plugin uses a socket to communicate with a Python script that controls the autofocus module and calculates the defocus (distance of target plane from current focal plane).  This Python script runs separately from Micro-Manager.