Standard Names and Colors for Beta Cell Segmentation
|3||Mitochondrial Membrane Outer||dark green||0||125||0|
Notice here that:
Your own group can and should build a similar table using standard names
from your field. Although difficult, it's also a good idea to try and use
the same ordering of object types across similar models, since most IMOD
analysis tools (such as mtk) require you to list the object's number. You can
renumber objects using: Edit > Object > Renumber....
Although there are (unfortunately) no enforced standards, a good standard to use in the field of cellular biology are the " NIF Vocabularies". NIF, an initiative at the University of San Diego California, provides the following website interface where you can being typing the name of an organelle and an auto-complete feature will suggest the appropriate name:
NIF ontology, they also provide a list of common subcellular compartments here:
Clicking on any of these organelles will link to information and often
pictures of that organelle. Note that each "object" in NeuroLex contains a
unique identifier. For example
Microtubule" has the unique identifier "sao1846835077".
Within IMOD each "Object" contains: many contours and these contours
are meshed together across the volume to form multiple surfaces.
Although many groups create a SINGLE object for each type of organelle.....
other groups prefer to segment each individual organelle (each surface) in a
new object. When you do this it's still important to name objects consistently,
and you may also want to add a number to the end, for example:
Segmenting Each Surface into a Separate IMOD Object
|Single Object (per organelle type)||Multiple Objects (one object/surface)|
Within IMOD you may often find yourself wanting or needing to create
objects which don't represent standard 3D structures. For example, you may
want to create an object with scattered points to show interesting features
within your tomogram, or an object with open contours to measure distances
between two types of organelles, or to show section boundaries, and so on.
For such "non-standard" objects I suggest you use capital letters to make
them stand out. I've listed some examples of these objects below:
Examples of Non-Standard Objects
|POINTS OF INTEREST||255||0||255||purple||When segmenting a cellular tomogram it's not uncommon to find interesting/unusual features which you want to show other people. To flag these interesting areas I recommend creating an object of type "scattered points", which you should call "POINTS OF INTEREST", set sphere size to about 20 and points per contour to 1. You may also want to add a label to each contour (to comment on what you see) by going Edit > Contour > Type... then enter a label. Next time your supervisor is around you can then use [c] to iterate through these points of interest, and see if any are biologically interesting.|
|MEASURING STICK||255||255||255||white||Use this to measure from one point to another. Make sure you set the object type to "open contours" and you may also want to increase the line width to about 3 and set points per contour to 2 so that each "MEASURING STICK" appears as a nice thick white line. After clicking two points (often spanning several sections) you can then measure the (selected) line's length by going: Edit > Contour > Info.|
|TOMOGRAM BOUNDARIES||0||0||255||blue||To just show a plain box around your boundary you can do so in the ModelView window via: Edit > View > Bounding Box, and you can change the color from yellow in the Objects dialog. However when I have multiple sections joined together in Z I sometime like to delimit/model the boundaries by creating a blue "TOMOGRAM BOUNDARIES" object.|
|UNKNOWN||255||255||0||yellow||Often during segmentation you'll see organelles which you are unsure of. In this cases it makes sense to create an object such as this. At a later time you'll want to go through this object with someone more experienced, and make sure you shift all surfaces from here into their appropriate object.|
|GOLD FIDUCIAL||0||255||0||green||Not often, but in some situations you may want to segment the gold
fiducial particles which typically occur at the very top and bottom of your
tomogram. To segment these you should use scattered points with a small
sphere size for the object. These gold particles are typically 10, 15
or 20 nm in diameter and appear as dark dots. They are NOT part of the cell,
but are often added to both sides of a section to aid in aligning tilt series,
and if done well their distribution should be quite uniform with no clumping.
NOTE: If you are doing fiducial tracking on a tilt series it's not really necessary to label your objects, because it's pretty obvious that all your objects/contours are gold particles.
|IMMUNOGOLD||255||200||0||gold||Immunogold labelling or Immunogold staining (IGS) is a staining
technique used in electron microscopy. Colloidal gold particles are most
often attached to secondary antibodies which are in turn attached to primary
antibodies designed to bind a specific protein or other cell component. It
can also be attached to protein A or protein G instead of a secondary
antibody, as these proteins bind mammalian IgG Fc regions in a nonspecific way.
Gold is used for its high electron density which increases electron scatter
to give high contrast "dark spots". To segment these, use a
scattered point object, with a small sphere size of about 1-5
(whatever fits best). |
NOTE: Although they appear the same, these gold particles are different from "gold fiducials" (which are used purely for alignment).
|MINDIST.Microtubules AND Vesicles||0||0||255||red||Using the program mtk you can automatically generate lines, representing the minimum distance between surfaces in two objects. If you come back to such objects in a few weeks time you'll forget what you did, hence I advise giving such objects long descriptive names!|
In this article I've explained the importance of naming conventions, and suggested a set of standards you should follow. To revise:
Each group should create a table of standard object names and colors for all the common compartments which students will need to name and segment.
- Standard object names should be:
- Spelt in full
- Title case
- Tied to a shared vocabulary such as the NIF ontology.
- some examples: "Free Ribosome", "Mitochondria Membrane Outer", "Peroxisome", "Autolysosome", "Nuclear Pore" ... and so on
- The Name Wizard IMOD plugin provides a nice interface to help you implement this table as a CSV file and use this to verify all your objects have correct names and colors.
- In cases where it make sense to use multiple objects per compartment type (such as one object per surface), use the same color and name, and use a period to separate the number.
- some examples: "Multivesicular Body.001", "Multivesicular Body.002", "Multivesicular Body.003", ... ... and so on
- For non-standard object (objects which don't represent cellular compartments), you can enforce your own standards, but I recommend using capitals to make them stick out.
- some examples: "POINTS OF INTEREST", "UNKNOWN", "MINDIST Golgi Apparatus AND Transport Vesicle WITHIN 50nm", ... ... and so on