Finished! Looks like this project is out of data at the moment!
Thank you all for your participation in this project! We are excited to share some key results in the following Blog Post. Also, see our Results Page where we share an in-depth overview of our results!
FAQ
What is an electron microscope?
A traditional microscope uses light to illuminate a specimen, whereas an electron microscope uses a beam of electrons. Using an electron microscope rather than a light (photon) microscope allows us to look at smaller objects. This is because electrons have a much shorter wavelength than photons, and so are able to distinguish smaller objects.
What can you look at using an electron microscope?
Electron microscopes can be used to study a huge range of biological specimens, from tiny molecules such as proteins, to larger structures such as cells or tissues, and everything in between. Electron microscopy can be used to advance our understanding of many different processes, such as how healthy cells grow and develop, how bacteria and viruses infect our cells, how our immune systems fight infectious diseases and cancer, how our brains work and how we age.
How do we study the feature of interest in the image?
An image taken with an electron microscope contains a huge amount of information. The information we want to extract from an image will depend on our particular research question. Until recently though, most electron microscopes could only give a 2D view from a very thin slice through a cell or tissue. This was a problem because humans aren’t very good at visualising 3D structures from a 2D image. Think of the difference between seeing a city on a 2D map, and actually visiting that city and moving through it and seeing how all the roads and buildings and rivers and people interact with each other in 3D.
How can we study specimens in 3D?
We can look at a cell in 3D using different types of microscope, the two we have used here are called a serial block face scanning electron microscope (SBF SEM) and a focused ion beam scanning electron microscope (FIB SEM). In these microscopes, the cell surface is imaged, and then a thin ‘section’ is cut away, and then the cell is imaged again. A diamond knife is used to cut the sections away in the SBF SEM and a highly focused beam of heavy ions is used in the FIB SEM. These microscopes can cut sections so thin that it would take 2,000-20,000 sections to cut through the width of a single human hair! This process of cutting and imaging creates a series of 2D images.
How can we generate a 3D model from lots of 2D images?
One way to convert these 2D images into a 3D model is to draw around the feature(s) of interest. This is known as ‘segmentation’. We also call it ‘advanced colouring in’!
How can this be used to generate a 3D structure?
A 3D model of the cell can be created by combining the segmentations from the series of 2D images produced by the serial block face scanning electron microscope. The individual segmentations are stacked together to create a 3D surface. It is much easier for humans to understand this 3D nuclear envelope, and to compare it to diseased nuclear envelopes, than it is to understand the 2D images showing a very small part of the structure. In the example below, you can just make out the individual segmentations as the approximately horizontal ridges on the 3D surface.
These are some examples of the common challenges you might encounter in this project
These are some examples of the common challenges you might encounter in this project.
Lipid drop or not?
If you're not sure whether a certain blob is a lipid drop try moving up and down through the 3D structure using the flipbook - sometimes seeing a slice above or below the one you're classifying on will clarify whether your blob is a lipid drop.
Don't forget to move back to your original slice to segment.
Lipid drops might also be confused with mitochondria.
In the above image, we have marked a lipid drop and two mitochondria (marked by 'm'). Lipid drops appear more circular than most mitochondria and have a darker outer membrane than mitochondria with a darker interior.
Merging lipid droplets.
In cases where lipid drops appear to be merging you should individually segment each of the drops, rather than a single segmentation of each drop.
Cropped lipid drops at the edge of the image
If a lipid drop is only partially visible because it is at the edge of an image then do not segment it. We have uploaded images that overlap enough such that each droplet should be fully contained in one of these. There is, therefore, no need to segment droplets cropped by the edge of the image since these will appear in full in other images.
In the image below those lipid drops marked with a red 'X' should not be segmented.
