mitochondria

Mitochondria analysis

Regulation of mitochondrion size in neurons affects synaptic plasticity (Divakaruni et al., 2018; Rangaraju, Lauterbach and Schuman, 2019), axonal and dendritic branching (Li et al., 2004; Bertholet et al., 2013; Courchet et al., 2013; López-Doménech et al., 2016; Lewis et al., 2018), and synaptic transmission (Sun et al., 2013; Kwon et al., 2018; Lewis et al., 2018). Here, we compare mitochondrion size across neuronal compartments and relate mitochondrial density within basal dendrites to their synapse density. We also give some basic tools for visualizing cells with their mitochondria within the reconstruction.

Analysis flowchart: solid boxes indicate data, dashed boxes indicate manuscript display items

Interactive Notebooks

• compartment_comparison.ipynb An analysis notebook comparing mitochondria across neuronal compartments (Figure 5C)
• distance_to_soma.ipynb An analysis notebook quantifying mitochondrial density and synapse density at different distances from the soma.
• visualize.ipynb A brief notebook that demonstrates a way to view a neuron rendered with its mitochondria

Base data

• pni_mito_cellswskel_v185.csv A dataframe that describes each mitochondrion that overlaps with one of the cells with a soma in the volume and a skeleton (filtered and formatted from the full mitochondrion dataframe)
• pni_mito_cell_overlaps_v185.csv A dataframe that describes how much overlap each mitochondrion has with each cell.
• pni_nucleus_segments.csv A dataframe that describes each predicted nucleus segment in the volume.
• pni_nucleus_cell_overlaps_v185.csv A dataframe that maps each cell to an overlapping nucleus.
• neuron_received_synapses_v185.csv A dataframe that describes the synapses received by each analyzed neuron (filtered from the full synapse dataframe)
• pyc_analysis_ids.csv A list of PyC ids with accurate compartment labels
• pyc_analysis_completesoma_ids.csv A list of PyC ids with accurate compartment labels and generally complete somas

Intermediate data

• pni_mito_analysisids_v185_fullstats.csv A dataframe that adds a surface area measurement, the mitochondrial complexity index, and an inferred compartment label for each mitochondrion in pni_mito_cellswskel_v185.csv that overlaps with the pyc_analysis_ids.csv. Created by scripts/computeextramitostats.py
• mitotoskel.h5 Contains associations between mitochondria and the skeleton nodes of each cell. Created by scripts/mitotoskel.py
• distancebinstats.csv Contains dendritic segment IDs, volume measurements and surface area measurement for each compartment branch of the analyzed cells. Created by scripts/computebasicbranchstats.py
• distancebinfullstats.csv A dataframe that adds synapse count, synapse surface density, mitochondrial volume, and mitochondrial volume density to the branch statistics in distancebinstats.csv. Computed by scripts/computedensitystats.py
• distancebinproximity.csv A dataframe that describes the proximity of each dendritic segment to the soma
• distancebindiameters.csv A dataframe that describes the approximate diameter of each dendritic segment

Scripts

See scripts/README.md and scripts/derivedata.sh for a walkthrough of how to compute the intermediate data.