Exploratory access to the EPSRC CONTRAST Facility
Four grants are available for CLIRPath-AI Network members to perform proof-of-concept studies at the Exeter EPSRC coherent Raman scattering facility (CONTRAST) to assess whether useful vibrational image data can be obtained on a clinical time frame. Each grant will cover up to five days of measurement time, facility access charges, full technical support and training from an experimental officer, travel (within the UK) and accommodation. Grants are only available for UK-based applicants who are members of the CLIRPath-AI Network and are eligible for EPSRC funding.
Coherent Raman scattering (CRS) exploits nonlinear optics enhance vibrational signals to enable real-time Raman imaging on the cellular scale; a capability that holds the key to the next generation label-free histopathology.
The CONRAST facility consists of two custom-built systems that offer cutting-edge CRS imaging capabilities beyond that available with state-of-the art commercial systems.
System 1 provides rapid hyperspectral CRS imaging using chirped femtosecond laser pulses to provide rapid hyperspectral acquisition while retaining the full speed and image quality of narrowband SRS imaging. Moreover, in this lab we have the ability to combine CRS with complementary techniques including second harmonic generation (SHG) and two-photon fluorescence (TPF), which provide complementary information about the collagen structures and endogenous fluorophores. The system is set up for 3D imaging, large area (i.e. sq cm) scans and rapid hyperspectral imaging.
System 2 provides broadband coherent anti-Stokes Raman scattering (BCARS) which enables both speed and spectral breadth. The system utilizes a configuration of laser sources that probes the entire biologically relevant Raman window (500–3500 cm–1). By utilising intra-pulse three-colour excitation and the non-resonant background to heterodyne-amplify weak Raman signals it is possible to obtain efficient acquisition of the typically weak ‘fingerprint’ region of the vibrational spectrum.
The facility is supported by a senior experimental officer (Dr Jessica Mansfield, Co-I) with over 15-years’ experience in CRS and nonlinear optical microscopy. Visitors will receive one-to-one training and spend a full week exploring the capabilities offered by the two systems. Following each visit, the applicants will receive remote support for data analysis for publications and grant writing.
Applications will the scored and ranked against the following criteria:
1. Scientific quality.
2. Alignment with the aims of the CLIRPath-AI Network.
3. Feasibility of the proposed methodology.
4. Potential impact on applicant’s career.
5. Potential to lead to publications and further funding.
Information on sample preparation
Imaging tissue sections: Tissue sections can be any thickness as long as they are still translucent and light can reach the detectors in the forwards direction. Samples are best mounted between 2 glass coverslips as this allows the optimal amount of light to reach the detectors, however we can also handle samples mounted between a microscopy slide and a cover slip.
Cell Imaging: We can image both fixed and living cells on this system. For living cells researchers also have access to our cell culture laboratory. Living cells are best imaged in at least 1inch diameter well plates with a coverslip bottom.
Samples can be prepared either fresh or fixed and there is no need to add exogenous labels, however on the spectrally focused SRS system, we can combine coherent Raman imaging with TPF imaging of fluorescent labels if this is required.
Other samples: If you have a different kind of sample you would like to image, please contact us. We will be able to do a trail imaging session to determine the best sample preparation technique.
Applications should be emailed to Prof. Moger (J.Moger (at) Exeter.ac.uk) using the CLIRPath-AI Project Application Form (linked below) before 5pm Friday 15th November 2024. Applications should have a clear statement detailing how access to the CONTRAST facility would address the aims of the CLIRPath-AI Network. Applicants are encouraged to contact Prof. Moger to discuss the feasibility and proposed methodology before applying.
NB for the email address to work, you must replace (at) with @, no spaces.
Funding to acquire new data
The AI community can only make progress on developing new analysis models if they have data to work on. At present there is a very limited number of data sets available and this is seen as a major barrier to further development. This call is therefore a targeted call for projects where the focus is to generate high quality data sets, of either Raman or IR hyperspectral images or maps, of tissue samples that have annotations and metadata associated with them so that they can be made freely available to the community. This call is looking for proposals where significant new data will be generated from a large number of samples (likely to be TMAs). We have £50k available and we would be able to fund one large project or several smaller projects. Please note that, in line with EPSRC policy, we can only award 80% of the cost of the project.
The closing date for proposals has now passed, but if you have a project you would like to discuss, please contact clirpath-ai (at) manchester.ac.uk
NB for the email address to work, you must replace (at) with @, no spaces.
Collection of existing data set
We are aware that several groups will have data sets, but for various reasons have not yet made these freely available or are available but are not easily findable. We therefore would like to hear from any groups who have significant data sets and would be happy to share these more widely. A small amount of funding may be available to get the data sets into a state where they could be made freely available to the community. This might require funding for pathology time to annotate a number of cores so that model training can be achieved. We would like to see as many examples as possible of data set that are fully compatible with the FAIR (Findability, Accessibility, Interoperability, and Reuse of digital assets) principles. Please note that, in line with EPSRC policy, we can only award 80% of the cost of the project.
The closing date for proposals has now passed, but if you have a project you would like to discuss, please contact clirpath-ai (at) manchester.ac.uk
NB for the email address to work, you must replace (at) with @, no spaces.
Pump-priming
We were awarded £400,000 to be allocated to pump-priming projects that would accelerate the integration of SHP, DP and AI. They were to be broadly aligned with our work packages but not limited to them. Applications were welcomed from anyone who was eligible for EPSRC funding and were based primarily on scientific excellence. Preference was given to those who were actively engaged with the Network and attended the Sandpit session where the Network Challenges were discussed. Seven out of eight projects have been funded, with each project being awarded a maximum of £50k. In line with EPSRC policy, 80% of the cost of each project was funded.
Applications are currently closed.
Training fund
A training fund is available specifically to fund post doctoral and early career researchers to spend short periods of time (up to two months) visiting and working in the laboratory of a network partner to gain experience in a technique or methodology not available in the home laboratory. Grants up to the value of £2500 can be applied for to assist with travel and accommodation.
Applications are open at all times.
Discipline-hopping conference fund
This is for network members to attend conferences that are interdisciplinary, or are not in the member’s normal area of expertise.
This fund will primarily be used for:
1. Groups working in spectral pathology to attend an international medical conference in oncology and pathology and DP. The aim is to present the spectral pathology work to new audiences who are unaware of these technologies
2. Clinicians and AI scientists who would not normally attend biomedical spectroscopy conferences, to actively participate in such events
It is anticipated that this may lead to new collaborations, new funding, and hopefully larger scale multi-centre clinical trials.
Summer School bursaries
We host a yearly summer school aimed at early career researchers working in either SHP, DP or AI, to get together and learn more about each of the disciplines. A number of bursaries will be available each year to heavily subsidise attendance.
For details please see the Summer School page.
CLIRPath-AI is an EPSRC funded Network
