Important
Please Read before Using the Data Files
I. CAVEAT: Diameter Measurements.
The data files were generated using a computer-microscope system (see below for references). The microscope was a Nikon Optiphot equipped with a x63 oil-immersion Zeiss objective. This lens provided excellent resolution of filled dendritic processes. However, it was often difficult to accurately measure the diameters of the finer dendrites in the thick tissue slices, particularly when the dendrites were covered with spines. In addition, because of the resolution of the computer monitor, the settings of the cursor used to measure dendritic diameters were limited. Thus, the diameter measurements given in the files here are overestimates.
We have not used diameter measurements in any of our published work, and we recommend that you consider them to be inaccurate. In contrast, the length measurements of dendritic segments are accurate to within a micron over a linear distance of at least 400 um.
II. Origin of data
These data files were generated using a computer-microscope system designed by Drs. John Miller and Rocky Nevin (G.A. Jacobs and R.H.W. Nevin, 1991, Anatomical Record, 231:563), and used in the Claiborne lab for digitizing hippocampal neurons directly from thick slices of tissue (B.J. Claiborne, 1992, in Methods in Neurosciences, Vol. 10: Computers and Computations in the Neurosciences; ed: P.M. Conn; and, L.A. Rihn and B.J. Claiborne, 1990, Dev. Brain Res. 54:115). The system design is similar to that of the Neurolucida system made by Microbrightfield.
The neurons were intracellularly injected with horseradish peroxidase and histological procedures were followed to ensure a dense reaction product in the filled dendrites (B.J. Claiborne, D.G. Amaral, and M.W. Cowan, 1990, J. Comp. Neurol. 302:206; and, L.A. Rihn and B.J. Claiborne, 1990, Dev. Brain Res. 54:115). Slices were cleared in glycerol, and shrinkage was minimal. Neurons were digitized directly from the thick slices. Except for the locations of the large spines called thorny excrescences on the CA3 pyramidal neurons (see Point type F below), the locations of spines on the dendrites were not encoded.
III. Structure of the Data Files
The data files are often headed by comments contained within a "C" comment delimiter set as below:
/*
COMMENTS
*/
These comments can be stripped off, and the data below then read.
B. Data file format
The data below the comment delimiters is formatted as in the following example:
Line_Number Point_Type X Y Z Diameter
1 S 0.00 0.00 0.00 #9; 5.25
1. Line_Number and Cell Connectivity
Connectivity of the cell is read line by line in descending order in the file – it is NOT read by the Line_Number above. (Line_Number is an internal number used by the system.)
2. Point_Type and Cell Morphology
The Point_Type denotes the morphological structure defined by the point.
S = Soma point. Denotes a point that is part of the outline of the cell body.
P = Primary dendrite point. Denotes the beginning of a primary dendrite as it exits the soma.
C = Continuation point (most common point). Denotes a point along a dendrite.
B = Branch point. Denotes a bifurcation.
T = Termination point. Denotes 1) the end of a dendritic process (one node of the most recent bifurcation point), or 2) the end of the soma - when the ‘T’ follows a Soma point or a Primary dendrite point and is the first ‘T’ in the file.
F= Thorny excrescence on a CA3 pyramidal neuron. This point may be treated as a ‘C’.
In general, the most recent branch point ‘B’ or primary dendrite ‘P’ is connected to the points that are closest to it in the file. So if a branch point ‘B’ is encountered in descending order in the file, the following continuation points are connected to one node of this branch point. A termination "T" later in the file closes this node. Points (‘C’ or ‘B’) that continue after that ‘T’ fill the second node. A termination ‘T’ after this point closes the second node of the branch point and points after this ‘T’ fill the second node of the second closest branch point in the file, etc…. When both nodes of the last branch ‘B’ are filled, any following terminations ‘T’ denote the end of the primary apical that gave rise to them. Any further points are attached to the second closest primary ‘P’ point in the file, or, if there are no more primaries to terminate, the ‘T’ denotes the end of the tree altogether.
Diameter: Denotes the diameter of process at that point. Note that this measurement is not accurate – see above.