SONATA reports¶
The goal of this document is to clarify the specification with respect to BBP needs. The original report documentation is located here
Spike file¶
Spikes are currently supported on the following model_type: biophysical, point_neuron.
Group |
Field |
Type |
Requirement |
Description |
|---|---|---|---|---|
/spikes/{population_name} |
timestamps |
float64 |
Mandatory |
The time when the spike is happening.
Units is defined by the |
/spikes/{population_name} |
node_ids |
uint64 |
Mandatory |
The node id of the cell spiking |
The population_name group has an HDF5 attribute sorting.
Possible values are none, by_id, by_time, note that this is an HDF5 enum:
The default order is by_time.
The i-th value of timestamps is a spike of the i-th node id cell in node_ids.
The timestamps dataset has a units attribute defining the unit of the timestamp.
Only ms is supported.
Frame oriented, element recordings¶
Compartment report¶
Group |
Field |
Type |
Requirement |
Description |
|---|---|---|---|---|
/report/{population_name} |
data |
float32 |
Mandatory |
The reported values.
Units is defined by the |
/report/{population_name}/mapping |
node_ids |
uint64 |
Mandatory |
The set of node ids (no duplicate). |
/report/{population_name}/mapping |
index_pointers |
uint64 |
Mandatory |
The offset for each node in the data field. |
/report/{population_name}/mapping |
element_ids |
uint32 |
Mandatory |
The id of the compartments as in NEURON. Ordered by compartment ids and grouped by nodes. |
/report/{population_name}/mapping |
time |
float64 |
Mandatory |
3 values defining start time, end time, and time step. end time is not part of the report. |
For a node node_ids[i], the data for all the recorded elements is determined by data[index_pointer[i]: index_pointer[i + 1]]. Therefore the length of index_pointer is the length of node_ids + 1 (as opposed to the shape define in the SONATA repository)
element_pos has mentioned in the SONATA paper is not supported at BBP.
The data field has a hdf5 attribute units of type string.
Hardcoded to mV for now at the BBP.
The node_ids field has an optional hdf5 attribute sorted of type uint8 (different from SONATA spec).
Default is 0 for not sorted.
This field is not implemented.
The time field has a property units of type string.
Hardcoded to ms.
Soma report¶
“Soma” report is a special case of compartment report where only the values for 1 compartment of the cell are reported. It can be reported at the soma or in the axon initial segment (AIS) depending on the configuration. In the case of multiple compartments for the soma or the axon, the one in the middle is used (as the split is an odd number). The element_ids are always 0.
Summation report¶
Summation report is similar to a compartment report. It usually reports a membrane current in nA (although the units field says mV).
Synapse report¶
In that case, the element_ids are the synapse ids with no particular order / grouping. The node_ids are the one of the post synaptic cells.
Bloodflow report¶
A particular type of compartment report for vasculature nodes. It is actually a set of 3 report files that store for each time-step 3 values per segment of the vasculature:
radius (unit: µm)
blood pressure (unit: µm^3.s^-1)
blood flow (unit: g.µm^-1.s^-2)
Extracellular report¶
Not supported.