Name Wizard Plugin Help
This plugin provides an interface to rapidly change the name and colors
of objects and (more importantly) verify that all your object names
and colors match a table of standards names and colors.
Giving ALL objects consistent and PROPER names
(that is, names taken from a "shared vocabulary") is critical,
because without this nobody in your group (let alone any computer/database or
collaborator outside your group) will be able to identify, compare, understand,
analyze, data mine, or share your model file - and odds are your
model will be deleted after you leave.
This plugin can also be used to reorder, merge, delete and duplicate objects,
however it's main advantage is that it can auto-complete and verify names.
To learn more about the important of using standard names read this article on
naming objects in IMOD.
Click here to see the
Name Wizard video tutorial on my
IMOD plugin page
What one student may (accurately) name "Mitochondrial Outer Membrane",
another may name "Mitochondria", "mitochondrion",
"Mito memb", "MITO23", "MT", "dark thing",
"green" or just leave blank. The idea of this
plugin is to discourage people from "making up" names and/or leaving objects
unnamed. The names you use should instead should come from an
authority/website such as
Neurolex or the
The Gene Ontology.
How it Works
When you open this plugin (via: Special > Name Wizard) it loads a
table of standard names and colors, plus optional hyperlinks, descriptions and
unique IDs from a CSV (comma separated value) file from one of the following
(1) in the "IMOD_CALIB_DIR":
.. or, if that doesn't exist:
(2) in the "IMOD_PLUGIN_DIR":
Note that the former file location is preferred because it will not get
overwritten when IMOD is reinstalled. By default these files contain just
over 200 entries from the
Subcellular Parts Table. To modify or add additional entries, you can
simply open the files in a text editor (like Notepad or TextEdit) or
spreadsheet program (like Excel). If you are serious about making your
group use consistent labels, I recommending installing the same
"standard_names_persistent.csv" on all computers in your group and making
sure all your models pass the Name Wizard test.
The Standard Names and Colors CSV Table
The current format for the standard names and colors csv file is:
(1)Name, (2)Red, (3)Green, (4)Blue, (5)Hyperlink, (6)UniqueID,
(7)Description, (8)Super Category, (9)Synonym(s)
Notice commas delimit the separation between each field. Below I've explained
these nine fields in more detail:
- Name - The name of your object/protein/organelle/compartment.
We highly advice you don't just "make up" names... they should be taken from
one of the authorities listed above. Another advantage of using these websites
is that you'll find all the other fiends (UniqueID, hyperlink etc) you need.
Names of objects/proteins/compartments should be in Title Case and
Singular. If you are creating a name for something more abstract we
recommend using UPPERCASE (eg: "MEASURING STICK", "GOLD FIDUCIAL").
- Red - The red component of your "standard color" for this
compartment - a represented by an integer between 0 and 255.
- Green - The green component of your "standard color" (as above).
- Blue - The blue component of your "standard color" (as above).
- Hyperlink - A hyperlink to information about and/or pictures of
- UniqueID - A string which uniquely identifies your compartment, and
is linked to an authority such as those listed above. Even if two different
groups/countries use different names/synonyms, these UniqueIDs help ensure
they map to the same thing, and tie into the context of larger rule-based
- Description - Here you can copy the description from an authority,
or may chose to include your own description of what the organelle looks like,
so that other people in your group can help identify them. Note you can
actually include image HTML markup, but be careful not to include commas!
- Super-Category - The super category represents what your
compartment is and/or belongs to.... for example: Mitochondrial Outer
Membrane "is part of" Mitochondrion.... OR Nucleus
"is a" Membrane Bound Organelle. In computer programming this is
important because the properties/rules of the supercategory can be applied to
all it's sub-category.
- Synonym(s) - Any commonly used alternative names for this
compartment, separated by semicolons.
To give an idea, here are two examples of valid entries:
Nucleus, 255, 255, 0,
http://www.neurolex.org/wiki/Category:Nucleus, sao1702920020, A
membrane-bounded organelle of eukaryotic cells that contains the chromosomes.,
Membrane Bound Organelle,
Mature Insulin Granule, , , ,
Insulin secretory granule which occurs inside pancreatic beta cells; is about
300 nm wide and contains a large electron-dense core, Insulin Granule, Dense
core granule;Mature granule
If you open the default files (standard_names.csv) you'll see many more
examples and also notice that it's possible to write comments by starting
a line with "#".
If you do add your own entries, the "Name" field is the most important
and mandatory field, however it is recommended you also enter
"Red,Green,Blue" (specifying your desired color for the compartment)
, a "Hyperlink" (a URL where information about or pictures of
the compartment resides), a "UniqueID" (taken from an authority
such as NeuroLex which links to an "ontology"), a "Description"
(to help your group members identify the object/protein/compartment)...
and you may also consider typing in the "Super Category" (helping
identify what the object is/the next level up), and finally any commonly
used "Synonym(s)" (common expressions/abbreviation you might use for
this object). Whenever an object name matches an entry, all the fields are
displayed in the tool tip when you hover your mouse over the green box which
appears. If you click the "match" it will open the provided hyperlink - hence
this hyperlink represents a valuable learning resource for students.
TIP: Since CSV files use commas (,) to separate fields, remember to
replace any commas you have within sentences with a semicolon (;).. otherwise
your text will load into the wrong field. Synonyms in the "Synonym(s)" field
should also be separated by semicolons, as demonstrated in the second example
The List of Object Names
In the Name Wizard plugin interface you'll see five columns:
- Color - Click this color box to quickly change the color. If you
wish to perform a "Selection" action
(eg: "Delete") you can select multiple objects using the check boxes. If you
click "Match Colors" all objects which have a match will change to the standard
color for that name (if one exists). This can be a handy time saver!
- Object Name - Notice that as you type it should auto-complete with
the full list of names from the standard names and colors CSV file/table.
Whenever a name matches one of these entries a "match" will appear. If you
want to preserve the match, but add extra information use a full stop (.).
This allows you, for example, to unique identify individual
objects/compartments by labeling objects "Axon.001","Axon.002" etc. Some
groups prefer to separate surfaces into separate compartments like this, but
many find it easier to manage to segment all axons in a single object
- Match - This column is red if you have no match, but changes to
green when you have a match. The "goal" is to try and have ALL your objects
match. Note that if it's light green then it matches a standard name, but
not the color. You can correct the color by holding your mouse over it to
see the red, green and blue values listed for that name (in the tool tip),
then clicking the color box to match these colors... or you can simply click
the "Match Colors" button at the bottom. If a hyperlink is provided for that
entry, then you can click "match" to open a URL matching the compartment
- UniqueID - If an object name has a match and a UniqueID is
provided for that name, then it will appear here. UniqueIDs are important,
as a way to uniquely identify a compartment/organelle/protein without relying
on the object name (since the names and classification of organelles change
surprisingly often over time).
At the bottom of the window you'll notice a few extra buttons.
- Refresh List - If you have added/removed or renamed objects
outside the plugin you should press this to refresh the list of names.
- Selection - This includes a number of options to
delete/merge/duplicate/reorder and batch rename all the objects which have
been checked. The options include:
- Delete Selected - Deletes all selected (checked) objects.
- Merge Selected - Merges all the contours from the selected (checked)
objects into the first object, and deletes the (now) empty objects.
- Duplicate Selected - Takes a single selected object, and creates
multiple new objects with the same properties (name, color etc) and can also
copy contours (if specified). NOTE: To split surfaces into new objects use
- Move/Reorder Selected - Used to quickly reorder objects, by moving
all selected objects together and down/up to the number you specify.
- Batch Rename (.001, .002, etc) - Batch renames all selected objects
and includes the option to append numbers to the end (NewName.001, NewName.002,
- Deselect/Uncheck All - Deselect/uncheck all objects which have been
- Select Range - Select/deselect objects within a given the range of
objects. Keep in mind however, you can also do this holding the [shift] key to
select or deselect a range of objects, starting from the last object
selected/deselected without [shift].
- Select Matching Names - Select/deselect objects matching a string
- Select Range - Select/deselect objects within a given the range of
- Find and Select Names - Select/deselect objects matching a string
- Recolor Selected Objects - Allows you to quickly set all
selected objects to a single color or a progressive gradient between two
- Apply Random Colors - Give random colors to the objects
you've selected. This feature can be useful to see if contours in different
objects belong in the same object in cases where you're attempting to have
only one surface per object.
- Match Colors - Click this to change the color of all correctly
named objects to match the color of their matching entry (if a color has
- Standard Names - Includes information about the standard names
and colors csv file, plus the option to reload this file. If you wish to
edit this file (to add your own entries) you should be able to click the first
option and chose to launch a text editor or spreadsheet program... although
it's probably just as easy to open it yourself by finding it in
This plugin was created by Andrew Noske (andrew.noske<at>gmail<dot>com).
If you encounter bugs please e-mail me before e-mailing the
IMOD group (to reduce traffic).
In your e-mail please tell me exactly how and when the problem
occurred and attach the model file you were using with
enough information that I can replicate the error/crash.
NOTE: This plugin is part of the is part of the
initiative. Please contact me for citation information.
Acknowledgements: Mark Ellisman and The National Center for
Microscopy and Imaging Research (www.ncmir.ucsd.edu) for helping sponsor
and encourage this work. Maryann Martone and the Neuroscience Information
Framework (www.neuinfo.org) for support and access to their ontologies.
David Mastronarde and the team at The Boulder Lab for 3-D Electron Microscopy
(bio3d.colorado.edu) for their wonderful support of all my plugins.