Open source software 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.

Under development

OPM image data acquisition software: we are developing 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.

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.

Open instrumentation

The technology developed in this project will contribute to the openScopes initiative, that aims to provide the know-how and open source software tools to implement a suite of open source instrumentation for light microscopy and related modalities that are intended to enable researchers to implement, maintain and upgrade advanced optical imaging capabilities at relatively low cost, including in less affluent research communities where technical support may not be available. These capabilities include FLIM, optical projection tomography, high content analysis and super-resolved microscopy. In general they can be implemented as upgrades to existing commercial microscope frames or they can be constructed around the new, cost-effective, modular openFrame platform, for which CAD files may be downloaded for laboratories to fabricate their own components or they can be purchased commercially.

openFLIM hardware: For a list of components to assemble a wide-field time-gated FLIM microscope system or an optical sectioning wide-field FLIM microscope utilising a Nipkow spinning disc confocal scanner, please download the openFLIM hardware list.

Under development

Optical autofocus module: We are developing an optical autofocus module that can be fitted to existing epifluorescence microscopes or to openFrame-based systems.

Quantitative phase contrast module: We are developing a pDPC kit that can be fitted to existing microscopes or to openFrame-based systems, which comprises a quadrant polarisation mask in 3D-printed holder that should be mounted in the transmitted light illuminator in the back focal plane of the condenser lens. This should be complemented by a polarisation-resolving camera and the open source software outlined above to provide single-shot semi-quantitative phase imaging that can be used for cell segmentation and morphometric analysis.

openFrame M3M: We are developing an openFrame-based HCA platform to provide automated multibeam multiphoton multiwell plate microscopy, including FLIM implemented with time-correlated single photon counting. This flexible instrument will also be configurable for other imaging modalities including spectral ratiometric FRET, quantitative phase imaging and polarisation-resolved imaging.