# Exploring lineages in the larval VNC
Matthew Q. Clark

## Goal

The goal of this lab is to understand how neural lineages help to build
functional circuitry. Though the function of some of these neurons isn’t
completely understood, having a connectivity map can help us generate
hypotheses about circuit function and also learn about the developmental
origins of these circuits

With a stable internet connection open
[CATMAID](http://tinyurl.com/larval-cns) to access the L1 brain. For
how-to movies see the [first part of this module](catmaid.qmd).

### Pick a lineage:

- NB3-3 (Wreden et al., 2017)
- NB5-2 (Heckscher et al., 2015)
- NB7-1 (Kohwi, Lupton, Lai, Miller, & Doe, 2013)

### Load the neurons that were studied in Mark et al. (2021)

Click on this widget: ![](assets/catmaid/icon01.png)

1.  Open Neuron Search widget (key binding `/`)
2.  Type in the “annotated” text field: **Mark et al. 2019**, push
    `enter`

#### Add neurons from your lineage to the selection table

<div id="fig-selection-table">

![](assets/catmaid/Add Neurons from your Lineage to the Selection Table.mp4)

Figure 1: Neurons from your Lineage to the Selection Table

</div>

Double check in your selection table that all the neurons from the
lineage are loaded\*\* [published lineage
neurons](https://drive.google.com/file/d/1JPg-cPQN9i4YtiMbE0aHh8WyEgmsy7vX/view?usp=sharing).

Open 3D Viewer widget (![](assets/catmaid/icon04.png), click on all the
neurons belonging to your lineage (e.g. A02b_a1l, A02c?\_a1l, A02e_a1l,
A02g_a1l, A02h_a1l etc.), click “Append” from “Neuron search” in the
selection table.

#### Rotate view and turn on Z plane 

<div id="fig-rotate-view">

![](assets/catmaid/Rotate View Turn on z Plane.mp4)

Figure 2: Rotate View Turn on z Plane

</div>

Tip: `Shift-click` at a point on the skeleton in 3D view to go to that
point in the EM stack

#### Is your lineage homogenous or heterogenous?

Does it contain motor neurons, interneurons, sensory neurons or a
mixture? Please show examples.

#### Find the entry point of the lineage into the neuropil and show it here:

#### Select a neuron that is the furthest from the entry point and one that is the closest.

Display them in different colors below

#### Is the neuron that is closest to the neuropil an early born neuron or a late born neuron?

Explain your rationale.

#### Do you think the early born neuron is part of the sensory or motor system?

Or a mix? Explain why:

#### Do you think the late born neuron is part of the sensory or motor system?

Or a mix? Explain why

#### For the early born neuron, show either a connectivity graph or display all pre- and post-synaptic neurons in different colors:

<div id="fig-connectivity">

![](assets/catmaid/Show a Connectivity Graph.mp4)

Figure 3: Show a connectivity graph

</div>

#### For the early born neuron, show either a connectivity graph or display all pre- and post-synaptic neurons in different colors:

For your pre- and post- synaptic of the early born neurons Export a
movie and save it to your folder

<div id="fig-export">

![](assets/catmaid/Export a Movie.mp4)

Figure 4: Export a Movie

</div>

## Useful widgets:

- ![](assets/catmaid/icon02.png) shows keyboard shortcuts
- ![](assets/catmaid/icon03.png) neuron search (‘/’ also opens this
  widget)
- ![](assets/catmaid/icon04.png) 3D viewer of selected skeletons (use
  this in conjunction with the ![](assets/catmaid/icon05.png) widget to
  manage list of skeletons)
- ![](assets/catmaid/icon06.png) Display network of connectivity

## Fun search terms:

- Whole motor neurons at A1 segment akira
- DNs from Brain akira
- DNs from SEZ akira
- et al

## Other papers that have associated published neurons:

- Zwart et al. (2016)
- Masson et al. (2020)
- Burgos et al. (2018)
- Eschbach et al. (2020)
- Carreira-Rosario et al. (2018)
- Miroschnikow et al. (2018)
- Zarin, Mark, Cardona, Litwin-Kumar, & Doe (2019)
- Mark et al. (2021)
- Berck et al. (2016)
- Eichler et al. (2017)
- Andrade et al. (2019)
- Larderet et al. (2017)
- Ohyama et al. (2015)
- Jovanic et al. (2016)
- Schlegel et al. (2016)
- Jovanic et al. (2019)
- Fushiki et al. (2016)
- Takagi et al. (2017)
- Tastekin et al. (2018)
- Imambocus et al. (2022)
- Kohsaka et al. (2019)
- Heckscher et al. (2015)
- Gerhard, Andrade, Fetter, Cardona, & Schneider-Mizell (2017)

<div id="refs" class="references csl-bib-body hanging-indent"
entry-spacing="0" line-spacing="2">

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<https://doi.org/10.1016/j.cub.2018.12.012>

</div>

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</div>

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</div>

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</div>

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</div>

<div id="ref-Jovanic2019" class="csl-entry">

Jovanic, T., Winding, M., Cardona, A., Truman, J. W., Gershow, M., &
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<https://doi.org/10.1016/j.cub.2019.01.009>

</div>

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</div>

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</div>