Current open source tools

FLIM data analysis software:  FLIMfit, our open source MATLAB-based software that provides a range of fitting techniques including global analysis. This will run on a standard personal computer or laptop but we recommend investing in at least 64 GB RAM and a  reasonable multicore processor if you intend to analyse large FLIM data sets. The FLIMfit software package is available as a client for the OMERO platform and can also be used as a stand-alone MATLAB application.

Wide-field time-gated FLIM data acquisition: our open source software, openFLIM-GOI, is a MicroManager plug-in and runs on a standard personal computer requiring ~8 GB RAM with USB and serial ports to interface with the equipment components.

FLIM high content analysis: our openFLIM-HCA software for automated multiwell plate wide-field time-gated FLIM (instrument control and data acquisition) using wide-field time-gated FLIM of samples arrayed in a 96 well plate is written in MicroManager.

AI-enabled software for analysis of 3D image data: This has been developed to work with time-lapse 3D image data from the OPM systems. Sentinal4D automatically learns and cluster cell shapes for morphometric analysis.

dOPM software: we have developed software to control the acquisition of OPM image data, including 3D single-cell resolved time-lapse spectral ratiometric FRET assays of arrays of live patient-derived organoids.

Under development

Open source HCA image data acquisition software: we are developing a MicroManager plug-in to control the acquisition of image data from pre-specified fields of view that will be identified in a pre-find scan of the multiwell plate. This is intended to work with multiple imaging modalities

Open source optical autofocus software: we are developing a software module to work with the optical autofocus hardware module and a microscope controlled by MicroManager. This will maintain focusing to enable automated imaging of multiwell plates or slides and will work with multiple imaging modalities.

Open source pDPC image data acquisition software: we are developing a MicroManager plug-in to control the acquisition of quantitative phase imaging data using pDPC. This will enable pDPC image data to be acquired with fluorescence imaging modalities during time-lapse assays such that the phase images can be used for single cell segmentation and tracking to generate masks to analyse the fluorescence data with single cell resolution.