Re: Meaning of ABA brain region spreadsheet columns

For the sake of completeness, Swanson lab did not define any nomenclature,
or part of it for ABA. As I said previously, ABA nomenclature and its
hierarchy are inspired from Swanson-2004. So, is exactly opposite. I am
not sure whether ABA used primarily or solely Paxinos/Franklin mouse atlas.

Regarding "cols G and H", I cannot say anything, because I haven't seen
the spreadsheet and I don't know what a PK is. Thus, I don't know what
"thalamus" ID is about in Bill's message.
Anyway, the unique identification or regions in BAMS is made by integer
ID's and not by abbreviations.

Mihai
On Sat, 3 Mar 2007, William Bug wrote:

> Sorry, Alan - got swamped with BIRN Ontology & Mouse BIRN AHM mtg
> preparations for next week.
>
> You are right - you & I reviewed details related to ABA image meta
> data last weekend - NOT brain region level meta data.
>
> I'd bet a lot of what Nigam lays out below  - RGB LUT values and PK -
> is correct.
>
>
> Region Abbrev (Cols B & C):
> 	'CNU' can be found in the Swanson (2004) XML file ("Cerebral
> nuclei").  Despite the ABA atlas gray scale image plates having been
> derived from the Franklin & Paxinos adult C57Bl/6 atlas, as Mihail
> mentioned, the Swanson lab did some region classification for ABA,
> and they lumped this at a higher level in a region they called
> "Cerebral Nuclei" - though, again as Mihail points out, Striatum
> immediately maps in rodent to a structure referred to as the
> "Caudoputamen" (http://brancusi.usc.edu/bkms/brain/show-braing2.php?
> aidi=129).  Caudoputamen [very important for the PD use case] and
> other structures in the base of the telencephalon are a part_of a
> larger structure they've defined for ABA as "Cerebral Nuclei (CNU)
> 	The one fly-in-the-ointment here is the phrase "...they've defined
> for ABA...".  This doesn't necessarily map to any of the other brain
> region classification schemes/CVs used elsewhere - not a trivial
> process - but not impossible - both the NN group and BIRN groups are
> working on this - as is Mihail - as he mentioned).  As Mihail points
> out - and you can see in the XML files he distributes - it does link
> into the vocabulary used in Swanson 1998/2004 for rat.  It most
> likely does not deterministically map to the CVs used for brain
> region by GENSAT (believe that somehow derived from some combination
> of NN and regions as given in the Franklin&Paxinos mouse atlas -
> believe the GENSAT segmentation was performed by someone from George
> Paxinos's lab who went to work with the Rockefeller GENSAT group).
> SenseLab has much less brain region detail.  It MAY be using the
> Swanson nomenclature.  Given SenseLab has just a subset of the
> regions you'd find in an atlas, it's possible someone there at Yale
> could fairly quickly provide a lookup table mapping their region
> terms to one of the other atlases (Luis may even have done this
> already in the context of some of the neuroinformatics repository
> integration work he has done over the last several years).
>
>
> Region color (Cols D, E, F):
> 	All digital atlas have a color LUT for regions.  These are generally
> just 8-bit (only because few atlas projects have foreseen having the
> expert personnel resources to manually segment > 256 regions) In the
> atlases, the regions derive from very laborious manual segmentation
> done in tools like AMIRA by specially trained, highly knowledgeable
> neuroanatomists.  The manual segmentation is performed on 2D
> sections, assembled into 3D volumes, smoothed, then added to the 3D
> atlas voxel data (many atlases are not actually TRUE 3D data sets -
> e.g., the Paxinos atlas used at ABA - so the re-assembly, smoothing
> and integration with voxels isn't required in that case).
> 	Anyway - ABA is obviously being forward looking and using 24-bit
> values for their region LUT.  Besides, when using Paxinos, they are
> GIVEN the region segmentation, so the manual effort is potentially
> eliminated (though the only electronic version of the region
> segmentation typically must be obtained through the atlas publisher -
> Elsevier in this case - and generally all the regions for a given
> Paxinos image (sagittal or coronal) are just lumped into a single,
> bit-mapped file.  This means you must take that bitmap, run
> algorithms to identify the individual regions (usually based on color
> - e.g., just as you see here, each region has a specified color in
> the bit map).  The isolated regions can then be converted to a
> geometric object format (from simple point list on to quad-tree or
> oct-tree) and this is then stored separately in a RDBMS.  This is
> EXACTLY what the SMART Atlas project in BIRN (from Maryann Martone's
> NCMIR group at UCSD - source of CCDB, too) has done.  This way, each
> individual region is defined as a geometry in a specified coordinate
> space AND - most importantly - can then be used to support SPATIAL
> queries on the atlas (e.g., "Show me all the defined brain regions
> that lie within this shape I just drew on image X that you've
> registered to your atlas coordinate space).
>
>
> Other Region numbers:
>
> 	A)  Cols G & H
> 		I would guess these are BOTH PKs of some sort as they both contain
> rather small and unique integers.  Given column G is listed in order,
> I'd guess that is the ABA internal PK for that region.  The other ID
> is probably a cross-reference to another brain region classification
> scheme.  A search of the various atlas classifications on the
> Mihail's BAMS site doesn't appear to provide such equivalent IDs.
> I've searched in NN, but those IDs don't correspond either (e.g., the
> Col H. for "Thalamus" - 351 - does not correspond to the NN ID for
> "Thalamus" - 283).
> 	One interesting note - if you sort the spreadsheet on Col H - you
> will find the rows are ordered in nearly perfect alphabetical order
> by brain region abbreviation.  This indicates to me these Col H
> values are likely to relate to IDs created for these regions by
> Mihail/Swanson when they did this classification work for ABA.  There
> are no integer PKs given in the BAMS XML files from the Swanson lab
> that match these numbers, so only Mihail can vet this hunch.  I'd
> guess they are expecting to use the "brain region abbreviation" as
> their immutable, unique link.
>
> 	B) Col I:
> 	Typically, the whole purpose of registering brain image stacks into
> the coordinate space of a digital atlas (such as has been done for
> the 20,000+ ABA image stacks for the individual, gene-specific,
> GenePaint-ed brains) is so the expert segmented regions from the
> digital atlas can be used to drive QUANTITATIVE ANALYSIS of the
> registered image stacks in a consistent and comparable manner.  Being
> able to visualize the atlas regions overlayed onto individual images
> from a given registered stack is useful for making qualitative
> observations - or as a pedagogical aid - BUT it can't drive automated
> analysis unless:
> 		- the atlas comes with a coordinate system and the segmented brain
> regions have been deterministically mapped into that space
> 		- the image stacks have been registered to the same coordinate space.
> 	In the case of the ABA, the atlas is the Franklin&Paxinos 2001 adult
> C57Bl/6 brain atlas and the coordinate space is their interpretation
> of stereotaxic coordinate mapping.  The registration process has some
> error (for ABA, I believe that is 300 microns [probably different for
> in-plane registration - i.e., 2D to 2D alignment - vs. the third
> dimension between images in a given dissection axis (i.e., coronal or
> saggital for ABA)]).
> 	SO - for Cols J,K,L, they likely refer to the location of the brain
> regions in the coordinate space.  In a true 3D atlas, all you'd have
> to do is give 3D geometric definition of the region shape (e.g., as
> an oct-tree), and give the location of the centroid for that shape in
> the coordinate system.  Since the F&P atlas is NOT a true 3D atlas
> but rather a series of 2D images, you don't have a 3D geometric
> definition of the region.  With that in mind, the way to specify
> WHERE in the atlas a given region lies is to give the FIRST and LAST
> atlas image plate the extents of that region lie in when viewed along
> a specific dissection axis.  For very convoluted structures such as
> the hippocampal formation, this can be a bit problematic to use
> computationally, but it's usually sufficient for the types of tasks a
> 2D atlas can support.
> 	In terms of what this set up can support, it is likely one of the
> things they are looking to do is to support users segmenting the gene-
> specific images (GenePaint-ed images) then comparing those gene
> specific segmentations to the brain segmentations.  Given the limits
> of the 2D realm, you can't really do true 3D volumetric
> intersection.  However, what you can do is determine to what extent
> regions-of-interest (ROI) created by users to identify expression
> patterns on a given GenePainted image overlap with the 2D sections
> through the brain regions that appear on the corresponding,
> registered Paxinos plate.  You would essentially try to estimate an
> intersection of the user drawn 2D ROIs with the 2D atlas region
> shapes for each region that appears on that Paxinos plate.  When
> sorting those numbers by atlas brain region, you'd then go through
> ALL the atlas images that contain a given region, and add up the
> total intersection with the user drawn ROIs across all the images
> from BRAIN X that user drew ROIs on.  This would be normalized to the
> total approx. pixel volume for that brain region across all the atlas
> plates where it appears - resulting in an APPROXIMATE volume ratio of
> a given gene stained for in BRAIN X with a given region defined in
> the atlas.  The large number - Col I - appears to scale with the
> approximate size of the region - e.g., "Olfactory areas" is quite
> large (838206), whereas one of the smaller regions included within
> OLF is much smaller (Nucleus of the lateral olfactory tract [NLOT] -
> 7407) - so I would guess this column represents that altas-defined
> approx. region volume (i.e., sum of all the 2D areas defined for that
> brain region across all the F&P atlas images).
>
> 	B) Cols J, K, L:
> 		It's quite likely ABA calculated an approx. 3D location value for a
> region probably truncated based on the existing locations of the
> Paxinos plates within the stereotaxic coordinate space.  Those
> coordinates would be specified either with:
> 			* a 2D coordinate location within a F&P atlas image plate (either
> as unitless PIXELS or as stereotaxically-defined MICRONS) + a unique
> ID for that F&P atlas image plate derived from a specific dissection
> plane axis (e.g., F&P Coronal plate 23)
> 			* a 3D coordinate location that somehow places some morphological
> property of the region in the stereotaxic coordinate space - e.g.
> front-upper-left point for the approx. 3D bounding box for that
> region, centroid for the approx. 3D bounding box for that region, etc.
>
> That's all I have time for now.  Must get back to meeting prep.  It's
> possible reading the ABA Nature paper from January would get you a
> more specific answer - or - better yet - just drop an email to the
> guy you spoke with at ABA.
>
> Hope that helps.
>
> Cheers,
> Bill
>
>
> On Mar 2, 2007, at 5:15 PM, Alan Ruttenberg wrote:
>
> > Don't recall doing this, though it's certainly possible that I've
> > forgotten.
> > Just to clarify, each of these lines is for a brain region, not for
> > an image.
> > If you want to do this later this evening with me, give me a call
> > at home after about 10.
> > -Alan
> >
> > On Mar 2, 2007, at 5:10 PM, William Bug wrote:
> >
> >> Alan,
> >>
> >> Didn't you and I review this already at the ABA site.
> >>
> >> All one would need to do is bring up one of these images at the
> >> ABA site, go through the "noodling" we did, and look at the
> >> corresponding entries in the spreadsheet to match up a "meaning"
> >> to each column (probably nearly all those columns).
> >>
> >> Cheers,
> >> Bill
> >>
> >> On Mar 2, 2007, at 2:15 PM, Nigam Shah wrote:
> >>
> >>>> BTW, if someone has a theory of what the other number in
> >>>> ontology.xls are, I'm all ears.
> >>>
> >>> Okay, pure guesses:
> >>>
> >>> Line 4 = Cerebral
> >>> cortex,CTX,CH,176,255,184,3, 85,4141526,61.647,29.999,33.711
> >>>
> >>> 176,255,184 seem like RGB values (they all range from 2 to 255) for
> >>> that region in the image.
> >>> 3 is a serial number or internal id.
> >>> 85 - no clue
> >>> 4141526 - no clue
> >>> 61.647,29.999,33.711 seem like 3D voxel coordinates.
> >>>
> >>> --Nigam.
> >>>
> >>
> >> Bill Bug
> >> Senior Research Analyst/Ontological Engineer
> >>
> >> Laboratory for Bioimaging  & Anatomical Informatics
> >> www.neuroterrain.org
> >> Department of Neurobiology & Anatomy
> >> Drexel University College of Medicine
> >> 2900 Queen Lane
> >> Philadelphia, PA    19129
> >> 215 991 8430 (ph)
> >> 610 457 0443 (mobile)
> >> 215 843 9367 (fax)
> >>
> >>
> >> Please Note: I now have a new email - William.Bug@DrexelMed.edu
> >>
> >>
> >>
> >>
> >
>
> Bill Bug
> Senior Research Analyst/Ontological Engineer
>
> Laboratory for Bioimaging  & Anatomical Informatics
> www.neuroterrain.org
> Department of Neurobiology & Anatomy
> Drexel University College of Medicine
> 2900 Queen Lane
> Philadelphia, PA    19129
> 215 991 8430 (ph)
> 610 457 0443 (mobile)
> 215 843 9367 (fax)
>
>
> Please Note: I now have a new email - William.Bug@DrexelMed.edu
>
>
>
>
>

Received on Saturday, 3 March 2007 23:41:02 UTC