IMOD - segmentation standards

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NOTE: This page is a daughter page of: IMOD


On this page I've documents list of recommended standards for the names and colors of cellular and sub-cellular compartments segmented using IMOD (or any other program for that matter). After five years experience segmenting objects, I highly recommend every group segmenting microscopic data should develop their own name/color tables like the ones below. By establishing standard colors early on, you not only allow consistency across your publications and any PowerPoint animations, but you help each member in your group instantly recognize organelles in other group members models (so they don't make fools of themselves). Different groups may chose/prefer different colors (as demonstrated in the examples below) - and this is quiet acceptable - but what what is NOT acceptable however is different groups using DIFFERENT names (or worse still nicknames/abbreviations) for the same type of compartments. Between groups names should be kept consistent and scientifically correct by using shared ontologies. More information about the importance of naming objects consistently is here:


Brad Marsh Group - Beta Cells

From 2005-2009 I did my PhD under with Dr Brad Marsh at the Institute for Molecular Bioscience in Brisbane, Australia. Here I used IMOD for the first time, and used a the following table of standard names and colors which I have linked to the standard names in Neurolex.


Standard Names, Colors and Segmentation for Beta Cells

Object Name Red Green Blue Color Segmentation Recommended Description / Comments
Plasma Membrane 255 60 255 pink Closed contours, linear interpolation Trace around the inner edge of the beta cell's plasma membrane
Nucleus 255 255 0 yellow Closed contours, spherical interpolation Trace the outer edge
Mitochondrial Membrane Outer 0 125 0 dark green Closed contours, smooth interpolation Trace outer edge
Multivesicular Body 255 155 0 orange Closed contours, spherical interpolation Look for multiple compartments
Golgi Apparatus 100 100 100 grey Closed contours, linear interpolation All but the trans-most cisternae, which we do in different color. In detailed models we may label seperate cisternae "Golgi C1", "Golgi C2" etc, from cis-to-trans face.
Trans-most Cisternae [1] 255 0 0 red Closed contours, linear interpolation Usually obvious to spot as more convoluted than other cisternae NOTE: This is not a standard name from NeuroLex
Microtubule 0 255 0 green Open contour, sphere size 2, draw along center. Unlike all others, segmented using open contour and then meshed into 22nm wide tube.
Mature Insulin Granule 0 0 255 blue Closed contours, spherical interpolation Typically spherical, ~300 nm dyameter, and has distinct dark crystal inside.
Immature Insulin Granule 70 170 255 light blue Closed contours, spherical interpolation Usually larger and much lighter in color than mature granules. NOTE: Neither Mature or Immature Insulin Granule existed in NeuroLex, so I added them using the wiki interface.
Transport Vesicle 255 255 255 white Scattered points (each sphere resized separately), but sometimes closed contours Typically small spheres, but can be elongated in some cells. Elongated vesicles should be put in separate object.
Centriole 255 255 0 yellow Open contour, with (each sphere resized separately) then meshed as tube with -2 diameter and no cap to produce tube of varing thickness. Are two (a monther and daugher) in almost every mammalian cell - typically perpendicular to each other and easy to recognize as they comprise of nine-triplets of microtubules in a barrel like shape.


Steven Fisher Group - Retinal Cells

Dr Steve Fisher studies retina cells at the Retinal Cell Biology Lab at the University of California, Santa Barbara. I met Steven in 2010 when he had just started using IMOD, but he'd already created a great set of instructions and color table for his students. Below is a copy of this table. What I thought was interesting is that Steven specified multiple colors for some objects. He found these "alternate" colors were useful to use in certain views to help distinguish and illustrate features in his models.


Standard Names, Colors and Segmentation for Beta Cells

Object Name Red Green Blue Color Segmentation Recommended Organelle Description from NeuroLex
Plasma Membrane 0 255 255 light blue Closed The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins (Gene Ontology).
Synaptic Vesicle 0 127 255 aqua Scattered Secretory organelles, some 50 nm in diameter, of pre-synaptic nerve terminals; accumulate high concentrations of neurotransmitters and secrete these into the synaptic cleft by fusion with the "active zone" of the pre-synaptic plasma membrane (Gene Ontology).
255 255 0 -
51 245 51 -
153 51 51 -
Post-synaptic Vesicle 153 10 225 purple Scattered A synaptic vesicle which has undergone fusion with the membrane of the pre-synaptic terminal (at the end of an axon) and released its neurotransmitters into the synaptic cleft.
NOTE: The was no entry for this in NeuroLex when I searched, so I added it.... adding new entries is quite easy - it even gives you a uniqueID. Entries are lated "curated" so if an entry is rubbish it will get deleted, or if an entry already exists (under a different name) they get merged.
255 125 255 violet
Large vesicles 255 0 0 red Scattered Vesicles of same size and content of coated vesicles; posited by Clooney et al. (2002) to represent coated vesicles after uncoating.
25 153 25 -
Cytoplasmic Cisternae 255 0 0 red Closed NOTE: Could not find an entry for this on NeuroLex... however I presume is for cisternae in the cytoplasm which are hard to identify further...
255 0 255 -
Ribbon Synapse 255 110 110 skin Closed contours, with some opened (using Contour > Type) Type of synapse characterized by an electron-dense ribbon, lamella (bar) or spherical body in the presynaptic process cytoplasm (Sjostrand, 1953; Ladman, 1958; Gray and Pease, 1971). It usually sits in or just above an evaginated ridge of the terminal membrane..." - Dowling (1987)
110 255 110 -
Mtochondrial Membrane Outer 85 255 0 green Closed The membrane on the outer surface of the mitochondrion, interfacing with the cell cytoplasm (Gene Ontology).
Mitochondrial Membrane Inner 255 170 0 orange Closed The inner membrane of the mitochondria. It is highly folded to form cristae (Gene Ontology). The inner membrane of the mitochondria. It is highly folded to form cristae (Gene Ontology).
Postsynaptic Process 0 0 255 blue Closed NOTE: Not sure what this object is - doesn't match anything in NeuroLex.
255 0 0 -
0 255 255 -
Multivesicular Body 0 60 25 dark green Closed A type of late endosome in which regions of the limiting endosomal membrane invaginate to form internal vesicles; membrane proteins that enter the internal vesicles are sequestered from the cytoplasm (Gene Ontology).



Technical Notes

Adding a table like the ones above to MediaWiki

Tables like the ones above can easily be created using any word processing or spreadsheet program, however I'd suggest the best place to put it is on a webpage within your group. If you happen to use a wiki/MediaWiki (like this website has done), here are some tips on how I generated the tables above. First I made a table in MS Excel with the following columns: (A) Name, (B) Red, (C) Green, (D) Blue, (E) Hyperlink, (F) Segmentation Tips, (G) Description. To generate a hexadecimal representation (eg: "#FF0000") of your colors (where each color is a number between 0 and 255) you should be able to use the following code in Excel:

=CONCATENATE(DEC2HEX(B2,2),DEC2HEX(C2,2),DEC2HEX(D2,2))

I've used these hexadecimal codes to color the background of the "Color" column. To generate the lines I needed for MediaWiki from my Excel Table I used this formulae:

=CONCATENATE("|- | [",E9," ",A9,"]|",B9," || ",C9," || ",D9," || style=",CHAR(34),"background: #",I9,CHAR(34)," color|",F9,"|",G9)

This worked pretty well, although I did have to then manually entered a return character after every isolated bar characters ("|") and replace the word "color" with the appropriate color. If you click "Edit" or "View" at the top of this page you'll see the MediWiki syntax I produced... or you can right click > "View Source" to see the HTML output. Don't hesitate to e-mail if you have questions or need further convincing of the importance of consistently colored/labelled data! -- Andrew.


Links

  • IMOD - a list of other wiki pages I've written about IMOD