INCF WHS Delineation Meeting Minutes
April 6-7 2010
April 6, 2010
Attendees:
PONS Oversight Committee Chair and Atlasing Oversight Member:
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Maryann Martone, University of California, San Diego, maryann@ncmir.ucsd.edu
Structural Lexicon Task Force:
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Douglas Bowden, University of Washington, Seattle, WA, USA,
dmbowden@u.washington.edu
Laszlo Zaborszky, Rutgers University, Newark, USA, zaborszky@axon.rutgers.edu
Atlasing Task Force:
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Seth Ruffins, University of California, Los Angeles, CA, USA,
sruffins@loni.ucla.edu
Other Participants:
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Mark Dubach, University of Washington, Seattle, WA, USA,
mdubach@u.washington.edu
Gully Burns, University of Southern California, Los Angeles, USA, gully@usc.edu
(lunch on the 7th)
Project Coordinator:
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Jyl Boline, Informed Minds Inc., Wilton Manors FL, USA, jylboline@gmail.com
Introductions and Goals of Meeting:
Goal of this meeting is to create a better set of WHS labels via a protocol that is
acceptable to both INCF PONS and Atlasing projects. We also want to set up concrete
deliverables and determine what will be needed for a contract.
Review general workflow and lessons learned:
Laszlo:
Laszlo gave an overview summarizing his mapping work, both manual and
computerized. He showed his cell mapping in 3D (used Jan Bjaalie’s 3D reconstruction)
and warped multiple brains together. They’ve also created a program to analyze the
density in the different areas (one voxel-based, one nearest neighbor based).
INCF WHS Delineation Meeting Minutes
April 6-7 2010
He also discussed some of the issues related to defining borders, as there are many
markers and the same marker isn’t always good for everything. We need to identify the
characteristics of the different markers. The MRI seems to have good fiber architecture
and we may be able to use the Nissl as a corollary. Whoever does manual delineation
will likely have different views.
Doug:
They wanted a 3D atlas that was composed of consensus parts as much as possible and
to visualize them on the web. Lessons he has learned during atlas construction:
 Think through everything the system will do and how before designing it
 Warp the midline to mid-sagittal plane and reflect one side to the other to
produce a symmetrical MRI (3D Edgewarp)
 Segmentation is best initiated in the coronal plane. Label each with the
appropriate acronym. Copy labels to the next section and edit them there.
 Work with voxelized images (use Photoshop or Amira)
 Work with individual voxels in three planes to edit discontinuities
 For boundaries not detectable in MRI, warp labels from an authoritative atlas
 Create multiple segmentation “modules” from which users can choose is most
appropriate to their data
He then went over the NeuroMaps workflow which is shown in the figure below:
INCF WHS Delineation Meeting Minutes
April 6-7 2010
Mark:
Mark showed the nearly completed atlas and mapper tool (available over the web),
Tracer is a stand-alone set of software (but can be set up on the web). Both Mapper
and Tracer are integrated with the database.
He then gave an overview of how to use Tracer. They do 150 micron voxel delineations
(some partial ones are excluded-based on a manual decision). He creates manual line
segments, and can create a curve. They can generate the labels in response to the
button click. They can assign and reassign colors if they wish.
Doug:
Doug reviewed the NeuroMaps software, which can be used to warp images onto an
atlas. His software is freely available and open source. In the software, you can add the
BAMS ontology.
Seth:
Gave an overview of his overall process when he creates an atlas and tips he’s learned
along the way. He starts with an MRI and a label file (label consists of an image and a
text header) and uses Amira.
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Toughs out the gross lines
Can interpolate these lines across multiple “slices”
Delineates the upper-level hierarchies first and then gradually does the next
grossest structures, etc. This ensures that every voxel is labeled, whether or not
it’s the final label. Also, the minute it’s done, people can use what’s there.
Each day’s work is saved in a new file, which ends up being a form of versioning
(useful for reviewing work if other operators are helping you)
Each operator has a folder, and they have their own history. If a lot of people
are working on the project, everyone starts with the full outline, and then
they’re assigned portions of it. All sets of label files can be merged into a single
file. If there’s an overlap, it calls it a merged conflict (and it becomes a new
dataset). A curator can go back and make a decision.
Outside of Amira, the label is split into a label image (Nifti) and label index (ID, color
abbreviation, name, and abbreviation are left blank at this point).
WHS Details:
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Discussion around potentially using Alan Mackenzie Graham’s mouse brain
delineations: the level of granularity is fairly gross. The atlasing group created
the WHS dataset specifically to allow multiple ways for people to bring in future
INCF WHS Delineation Meeting Minutes
April 6-7 2010
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datasets, it is also independent of the efforts, created specifically for the purpose
of the group. It has segmentations that were created from Al Johnson’s
automatic segmentation routine which could potentially be used for the first
pass for these segmentations.
T1, T2, T2*, Nissl (although it’s not perfectly registered to the MRs)
o 20 micron
o coronal has over 1000 slices
MR seems to have a fiber-based typed staining
Specimen:
o Original WHS is an individual animal dataset
o Probabilistic atlas is recently available
Are the voxels too small, will we actually want to downsample the dataset?
o Doug and Mark have the original and a downsampled version of WHS
o Amira does allow interpolations of labels across multiple sections
File size: Seth converted it to 8 bit data, which reduces the size by ½. He’s
passing around this dataset.
What we need:
We need to create a WHS PONS-approved label dataset along with documentation,
although we don’t need anything nearly as detailed as the ABA atlas. We will use the
pan-mammalian hierarchy generated by the PONS group for the structure names.
Level of granularity:
 Current WHS delineations (~30-40, we can probably use these as first draft)
 Mammalian rosetta stone structures (e.g. 100, 150 structures)
 What structures do people query on? ~30-40 that people use originally
 We can probably agree on about 50-100 structures that are the initial set of
consensus structures (equivalent across species), although we don’t need this
level of granularity to start.
 It is possible that in the future, other experts will come in and delineate.
NeuroMaps does something like this, it acts like an image-based wiki.
Structure Hierarchy Discussion:
Pan-mammlian hierarchy: which structures have already been “approved.” For
instance, “basal ganglia” isn’t necessarily in the primary hierarchy, but it should be
defined (by the structures that are considered part of it). For Kobe and SfN, show a
recommendation for the pan-mammalian nomenclature, here’s what we do when we
come to species differences, here’s what we do when we have an aggregate term. This
should be useful for informatics, but less so for anatomists.
INCF WHS Delineation Meeting Minutes
April 6-7 2010
We need to be able to cross rodent to primate using the Pan-mammalian consensus
structures. We need a chunk of brain tissue that corresponds to the structure starting in
WHS. This can also be used to bind the different nomenclatures together.
To present the actual hierarchy, those that are cross-species will be in the hierarchy, and
the others will be marked as being in that species (perhaps shown in a color), those that
aren’t will also be identified (perhaps an X). We also need a “not otherwise specified,”
smallest superstructure that we can name that includes that other entity. We should
create a PONS recommendation for how to deal with the species issue.
How comfortable are we with the “rosetta stone” structures? It currently contains the
primate structures in BrainInfo and should be suitable pan-mammalian, about 5-7% are
undetermined (we should contact Paxinos and Swanson about this to check). More
details about this needs to be determined by the SLTF.
Protocol Decisions:
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File type will be Nifti (as is WHS) and placed in WHS
o Will be treated as an interoperable “atlas” that is used for computation
o Will be distributed along with WHS at the INCF space
Use Voxel labeling
Use at least all 3 versions of MRI when doing the labeling (switching back and
forth), and hopefully the Nissl to some extent
Use primarily one plane (possibly horizontal, it has fewer slices) and switch back
and forth between the other two to check and “smooth” the structure outlines
Supply a set of criteria for delineation:
o Set up rules for delineation. e.g. in most cases, use rule #1, when rule #2
breaks, rule #3. We won’t necessarily have these today, but these should
be put in place in the contract and fine-tuned during delineation
Color: doesn’t matter what he uses to delineate, but they should be changed
before release
Start with review of structures in Rosetta stone structures and current WHS
delineations (from Al Johnson’s group). Laszlo may be able to modify them
Start labeling gross structures, then the smaller structures iteratively
o Start with Brain (should be done automatically)
o Go down each branch to wherever there are species differences and
count how many there are, even if we start with just the top 20
o Laszlo can look at the datasets and the hierarchy to see how far down he
thinks it may be possible to delineate this dataset. This would give us a
general idea of the # of structures possible to delineate (e.g. 11
INCF WHS Delineation Meeting Minutes
April 6-7 2010
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structures 3 levels down, under those, choose a few key structures and
leave everything else as unspecified within that structure for now)
o If there is a delineation called “brain” it gets “cannibalized” by smaller
structures because there is no hierarchy. But you may no longer have a
label called brain, instead it will be composed of all sub-structures
Add left and right in front of the structure name, include a parent structure that
contains just the structure name without left and right
Dealing with ambiguous terms in the hierarchy:
o Some belong in the hierarchy, but they wouldn’t be required for
delineation in the WHS (e.g. basal ganglia)
o We can define a set of terms that aren’t in the primary hierarchy that can
be delineated
o Doug is willing to prune everything up to where he thinks it can be
specified in this task
o May be able to only go down to a certain level for awhile, as the
hierarchy may be up for debate yet
Keep a notes page for:
o Each structure
o Each page
o Keep track of which landmark was used for delineation, especially for fiat
boundary (ones where a line is pretty much just drawn to help put in a
boundary, arguable but defensible)
We will bring the following issues to the atlasing group and see what they
recommend, and see if they can help us with whatever is needed.
o Full vs. half brain delineation
o Warp the midline of the brain to the biological midline
Create a formal WHS delineation protocol document as another deliverable
(ensure it gets added as part of the contract)
Questions and Recommendations:
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How many structures?
o Doug will send a document with a small subset of “safe” consensus
structures to start, once those are done, review what’s next
o As a comparison, 40-50 regions identified by Paxinos in the mouse/rat
o Potentially include a rough cortical map
Approximate amount of time for delineation?
o Mark: monkey brain, 3 ½ years but he’s been doing other things
o Seth: ~45 min for a student using an existing atlas
o A few minutes for Laszlo to curate
INCF WHS Delineation Meeting Minutes
April 6-7 2010
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o Might have someone else do much of the work, Laszlo mostly review it
Hemisphere delineation-just delineate one or both?
o One hemisphere:
 People may want to “hang” data on the atlas may wish to use only
one half of the brain.
 Produce a half brain first and then mirror it to produce the whole
brain
 Less time consuming
o Both hemispheres:
 There may be a problem with informatics when you have only half
the brain delineated
 Not necessarily more time consuming using Seth’s methods
 Produce a full brain first and then it is easy to create mirrored half
brains as needed (they can be stored and treated as separate
atlases)
o Given that the methods Seth uses do not take much more time, and we
have the ability to manage set up an atlas-based infrastructure post-hoc,
it would be better to delineate the whole brain now, rather than have to
go back later and do the rest.
The plane used for the majority of delineations, is up to who is doing the
delineations, but all planes should be consulted regularly
Ultimately it would be good if all the atlases and all the animals had the same
protocol for colors in relation to structures (even though any color can be used
while delineating). Is it possible to copy the ABA grouping to a certain extent?
Fiat boundary can be “solved” using classic gross dissection method (create your
own line). This creates structures that can work with microarray dissections etc.
Could potentially go back and forth between Amira and NeuroMaps, the data
types are compatible
Discussion of Contract:
Some concern about timeline and milestone:
Perhaps to deal with this, the contract can be small, where the first phase can be more
exploratory, even if it’s just the first set of structures and to nail down the protocol.
After that, the next versions can be ramped up to handle the delineation of more
structures.
Potential Schedule:
 Probably start in late May. June, or July to get going
 A day or two to write the contract
INCF WHS Delineation Meeting Minutes
April 6-7 2010
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Probably work 2 weeks continuously, until around after Kobe or perhaps a day
per week for a year. However, INCF doesn’t pay for time put, but rather for
deliverables. Proposal should reflect what you are willing to produce.
April 7, 2010
Attendees:
Doug, Mark, Laszlo, Seth, Jyl
The group started the morning trying to get Tracer set up on Laszlo’s machine, but there
were problems with Java. He was able to use it on Mark’s computer a bit.
Seth demonstrated using Amira, he also had some computer problems.
The group broke for lunch and met with Gully Burns. Discussion included some INCFrelated projects and how the different efforts represented by the people present might
fit into the overall INCF goals.
After lunch, the original group reconvened to work more with the software tools for
another hour.