HDF5 Version 1.3 Morphology Description

Changelog

  • 1.3 Added specification for Dendritic Spine.

  • 1.2 Added specification for Mitochondria and Endoplasmic Reticulum morphology.

  • 1.1 Added versioning to the file. Modifications to support glia cells

    (cell_family attribute and perimeter dataset).

  • 1.0 Initial format documentation.

History

The HDF5v1 format was conceived internally to the BBP to represent morphologies more compactly, instead of using the Neurolucida ASCII format. It uses hdf5 to store all the data needed to represent a neuron morphology. It follows the conceptual structure of the Neurolucida representation, but has a more accurate representation instead of relying on ASCII serialization of floating point numbers.

File Format

The file contains a root /, with three HDF5 Datasets that describe the Neuron or Glia cell morphology and dendrictic spine morphology. The /organelles group has 2 sub-groups that contain information about cell organelles and one sub-group that contains dendritic spine organelles. There is a mitochondria group that contains three HDF5 Datasets describing the mitochondria morphology present in the cell. Similarly, there is a endoplasmic_reticulum group that describes ER morphology. There is a postsynaptic_density/points dataset that describes dendritic spine PSD. There are also attributes in the /metadata group.

Note : The organelles group and the groups and datasets in it are optional and are not a must for representing cell morphology. These fields may be used when additional information about the organelles in the cell is available.

The datasets in the root / are:

  • points:

    A 4 column data set composed of 32 bit floating point numbers representing morphology points, which are basically the position and diameter at a cross section. The first three columns represent X, Y, and Z positions and the last column represents the Diameter, all in micrometers. Implicit in the points dataset is an index, starting at 0, of each point.

    Note: Points on the boundaries between sections are duplicated, such that the start point of a child section is the same as the last point of its parent section.

  • structure

    This dataset describes all the sections. It is composed of 3 columns: start offset, type and parent ID. Implicit in the structure dataset is an index, starting at 0, of each section.

    • start offset: The implicit index in the points dataset of the first point of the section. The points in this section go until the next Start offset defined by the next row in the structure dataset, except for the last section in the file, then it runs until the end of the points dataset.

      Note: When there is an ambiguity as to where the initial section starts, as in the case of single point branches from the soma center, it should be taken to be the soma center.

    • type: The type of process for this section. This integer is interpreted differently depending on the cell type.

      For neurons the values are: 1: soma, 2: axon, 3: basal dendrite, 4: apical dendrite.

      For glia cells the values are: 1: soma, 2: glia perivascular process, 3 glia process.

      For dendritic spine the values are: 2: neck, 3: head.

    • parent index: The implicit index into the structure of the parent. For the soma Type, it is set to -1, otherwise it must point to a previous section (ie: no forward references)

  • perimeters (optional for neurons and dentritic spines, mandatory for glial cells):

    Glial cells are not as tubular as neurons, therefore a truncated cone representation is not sufficient to capture both the lateral surface area and the volume of the process segent. So perimeter encode its lateral surface area. A 1 column data set composed of floating point numbers representing the perimeter of the cross section at each point. There is a one to one correspondence between this dataset and the points dataset. The unit is micrometers. The perimeter for the rows corresponding to soma points must be set to 0.

There are 3 groups in /organelles:

  • endoplasmic_reticulum

  • mitochondria

  • postsynaptic_density

The datasets in the organelles/endoplasmic_reticulum group are:

  • section_index:

    This dataset represents the index of the section that the ER lies in.

  • volume:

    A 1 column data set composed of floating point numbers representing the volume of the part of the ER lying in section referenced by the corresponding row in the section_index data set.

  • surface_area:

    Similar to the volume data set, this data set represents the surface area of the ER in each section in the section_index data set.

  • filament_count:

    This 1 column data set is composed of integers that represent the number of filaments in the segment of the ER lying in the section referenced by the corresponding row in the section_index data set.

The datasets in organelles/mitochondria group are:

  • points:

    This dataset consists of 3 columns and provides structural information about mitochondrial segments.

    • section index: The index of the section (as described in the structure dataset) that the mitochondrial segment starts in.

    • relative distance: The particular point (within the section defined in the first column) of the mitochondrial segment, as normalized distance in the range [0,1] from the beginning of the section.

    • diameter: The diameter of the mitochondrial segment at that point.

      Note : The branching points, on the boundary between 2 mitochondrial sections, are duplicated.

  • structure:

    This dataset describes the actual structure of the mitochondria by grouping the points described in the mitochondria/points dataset into mitochondrial sections.

    • start offset: The implicit index in the mitochondria/points dataset. It is similar to the start offset in the /structure dataset, as the points in this mitochondria go until the next start offset described by the next row in the mitochondria/structure dataset, except for the last mitochondria section in the file, then it runs until the end of the mitochondria/structure dataset.

    • parent index: This index number is similar to the parent index in the /structure dataset. It refers to the implicit index in the structure of the parent, and points to the previous mitochondrial section it is linked to. For each new mitochondria that is not linked to any other section, it is set to -1.

The datasets in the organelles/postsynaptic_density group are:

  • section_index (int): This column represents the index of the section that the PSD lies in.

  • segment_index (int): This column represents the index of the segment within the section that PSD lies in.

  • offset (float): This column represents the fraction of the segment where the PSD is located.

The attributes in the /metadata group are:

  • cell_family_enum: An H5 enum that can take the values NEURON, GLIA or SPINE.

    Inside each family there can be multiple types, this classification is out of the scope of this file.

  • cell_family: An H5 attribute of type cell_family_enum: States the

    family that the morphology belongs to. Prior version 1.1, the cell family is assumed to be NEURON. As of version 1.3, the cell family can be SPINE.

  • creator: The software used to create the morphology.

  • creation_time: date & time when the file was written

  • software_version: major.minor.patch.sha1 of the software that wrote the

    file

  • version: An attribute array of two U32LE integers that stores the major

    and minor version numbers. The version number has to be interpreted as follows: Versions with different major number are not expected to be compatible. APIs should be able to evolve gradually to newer versions, but parsing code may need to be very different. When the minor version number is increased, the new file format is guaranteed to be backwards compatible with parsing code for previous versions (or the other way around, parsing code for a version is forward compatible with file format minor revisions).

Geometric interpretation

Soma: there is only one soma section, however, different tools interpret them differently. Note: Dendritic spine morphology has no soma:

  • The series of points belonging to this section is a polyline that represents the outermost contour of the soma as seen down the Z axis (this is not exactly a XY plane projection because not all points may have the same Z coordinate). The chain is closed by joining the last point of the section with the first one.

  • A sphere, with the center at the geometric mean of all the points, with diameter of the maximum distance between two points.

Cell processes: Processes (called neurites in neurons) consists of a set of sections organized in a tree structure where the root is the soma, and each one consisting of a set of points. A section has one type of process assigned as a whole. Two consecutive points in a section define a segment. A section must begin at a root point or a branching point, and end at a branching point or an end point.

The diameter at an end point of a segment represents the thickness of the process at this point, and can be thought about as a sphere.

Note

The same set of points with different indices and a different structure dataset may represent the same neuron. For instance, swapping the order of how the neurites are included in the file, give two equivalent representations of the same neuron with different indices. For that reasons no assumptions about the order of enumeration of sections should be made.

Endoplasmic Reticulum: The ER extends throughout the cell body as numerous filaments. It is generally thought of as a single connected compartment. Thus, it’s morphological information includes the surface area, volume and number of filaments, as a property of the section of the cell body it lies in.

Mitochondria: The mitochondria are present as tube-like structures inside the Neuron cell body, and may extend through different sections of the neuron (Soma, axon, dendrites). There may also be multiple mitochondria present within a single neuron. Thus, they are represented as a tree-like stucture, with a series of points (which differ in radii), organized into sections. The position of the points are represented as a function of the section of the neuron they lie in. In case of branching mitochondria, multiple sections would be required to represent them while a single section would be sufficient to represent a mitochondria that does not branch.

Dendritic spine: Sections start at the root, a branching point or anywhere along a branch (ie: unifurcations are allowed). Two sections can share a single branch if they have a different section type. A spine base is defined as the first point of the root section. The spine base begins at the dendritic shaft and not the center of the dendrite. Unifurcations are allowed so that for a long morphological process that does not branch different sections can still be annotated as head and neck. PSD: postsynaptic density are identified on points.

Example

For the example, we will be using this simplified morphology (note the shared points in black: these are duplicated):

Example Morphology

points structure (note the implicit i index, the colours refer to the above diagram):

i

X

Y

Z

D

Colour

0

1

1

0

0

Red

1

-1

1

0

0

2

-1

-1

0

0

3

1

-1

0

0

4

0

5

0

2

Green

5

2

9

0

2

6

0

13

0

2

7

0

13

0

1

Blue

8

2

13

0

1

9

4

13

0

1

10

3

-4

0

2

Grey

11

3

-6

0

2

12

3

-8

0

2

13

3

-10

0

2

14

3

-10

0

1

Mustard

15

0

-10

0

1

16

3

-10

0

1.5

Maroon

17

6

-10

0

1.5

18

0

13

0

2

Light Blue

19

0

15

0

2

structure Dataset, where SO is Segment Offset, PID is Parent ID and TYP is Type (note the implicit i index):

i

SO

TYP

PID

Colour

0

0

1

-1

Red

1

4

2

0

Green

2

7

2

1

Blue

3

10

3

0

Grey

4

14

3

3

Mustard

5

16

3

3

Maroon

6

18

2

1

Light Blue

perimeters structure

perimeter

0

0

0

0

7.4

7.2

7

4

3.5

3.5

7.2

7

7

3.7

3.6

5.2

5.4

5.6

5.9

/organelles/mitochondria/points Dataset

i

SectionID

RelativeDistance

Diameter

0

1

0.25

0.4

1

1

0.7

0.8

2

2

0.8

0.65

3

1

0.8

0.32

4

6

0.5

0.9

/organelles/mitochondria/structure Dataset

i

StartOffset

PID

0

0

-1

1

3

0

Dendritic spine example

For the example, we will be using this simplified spine morphology.

Example Morphology

points structure (note the implicit i index, the colours refer to the above diagram):

i

X

Y

Z

D

0

0.1

Green

1

2.4

9.1

0.2

2

13.2

0.15

3

13.2

0.2

Red

4

15.9

2.4

5

13.2

2.3

Blue

6

2.4

13.2

2.8

7

4.03

13.2

2.4

structure Dataset, where SO is Segment Offset, PID is Parent ID and TYP is Type (note the implicit i index):

i

SO

TYP

PID

Colour

0

0

2

-1

Green

1

3

3

0

Red

2

5

3

1

Blue

postsynaptic_density Dataset

/organelles/postsynaptic_density/section_id structure

i

SectionID

0

1

1

2

/organelles/postsynaptic_density/segment_id structure

i

segmentId

0

0

1

1

/organelles/postsynaptic_density/offset structure

i

Offset

0

0.8525

1

.9

Consumers

Producers

  • morphology release