Available Services

The Volumetric EM service provides segmentation and analysis of structures in serial EM section data. This service is restricted to segmentation and analysis of a finite number of structures per image (ie, mitochondria, organelles, vesicles, other similar objects of study). The proposal must include specific examples of the structure(s) of interest in order to judge feasibility.  This service includes, but is not necessarily limited to, the following use-cases:

• Data pre-processing: de-streaking, alignment, contrast adjustment.
• Data annotation: generating dense labels covering structures of interest for the purpose of training AI algorithms.
• Model Development: Training and deployment of AI segmentation algorithms specific to the research question.
• Downstream Analysis: Analysis of segmented structures, morphology, number, distribution.

While these are examples of the services we can provide, we anticipate that most projects will require some combination of tools and services and so we will work with successful Applicants to craft pipelines that fulfil their analysis needs, as well as provide training and support in their future use. Our ethos is to work openly and transparently with our Users in the spirit of scientific collaboration. During the application phase, it will only be necessary to describe the data and the desired form of the analysis result; the precise details of the analysis will be discussed with the Applicants upon selection of the project.

Light microscopy analysis encompasses the analysis of data generated by any light microscopy modality (ie, brightfield, phase contrast, widefield epi-fluorescence, confocal, lightsheet, etc) and across any sample type.

The services we provide include, but are not necessarily limited to, the following use-cases:

• Image restoration and denoising: Removal of pixel-independent noise from images to increase signal-to-noise ratio (SNR).
• Semantic and Instance segmentation: Identification and segmentation of objects in an image, generation of image masks.
• Quantitative Image Analysis: Quantification of intensity levels in images or segmented objects.
• Morphometric Analysis: Analysis of shape and morphology of segmented objects.
• Custom pipeline development: Construction of an analysis pipeline combining two or more individual steps.

While these are examples of the services we can provide, we anticipate that most projects will require some combination of tools and services and so we will work with users to craft pipelines that fulfil their analysis needs, as well as provide training and support in their future use. Our ethos is to work openly and transparently with our users in the spirit of scientific collaboration. During the application phase, it will only be necessary to describe the data and the desired form of the analysis result; the precise details of the analysis will be discussed with the users upon selection of the project.

Cryo-Electron microscopy analysis encompasses the analysis of cryo-electron microscopy data, both single particle and tomographic reconstruction. This service includes, but is not necessarily limited to, the following use-cases:

• Single-particle analysis (SPA): Development of image processing pipelines for the reconstruction of single particle 3D density maps, starting from cryoEM raw datasets or pre-processed micrographs/particles. Map validation.
• Atomic Model Building: De novo model building from reconstructed 3D density maps, fitting of existing atomic structures and refining of atomic models. Model validation.
• Analysis of Flexibility and Heterogeneity: Development of image processing pipelines for local reconstruction and refinement of flexible regions and evaluation of the conformational heterogeneity landscape of the macromolecules.
• Tomography reconstruction: Development of image processing pipelines for the reconstruction and analysis of tomograms, starting from tilt-series containing fiducial markers or fiducial less. Segmentation of the tomograms and sub-tomogram averaging (STA).
• Custom pipeline development: Construction of a computational pipeline combining two or more individual steps.

While these are examples of the services we can provide, we anticipate that most projects will require some combination of tools and services and so we will work with successful Applicants to craft pipelines that fulfil their analysis needs, as well as provide training and support in their future use. Our ethos is to work openly and transparently with our Users in the spirit of scientific collaboration. During the application phase, it will only be necessary to describe the data and the desired form of the analysis result; the precise details of the analysis will be discussed with the Applicants upon selection of the project.