Search found 11 matches

by DavidSwygart
Mon May 11, 2020 10:45 pm
Forum: Anatomically detailed models
Topic: morphology altered when Import3d exports to CellBuilder
Replies: 4
Views: 608

Re: morphology altered when Import3d exports to CellBuilder

The error was due to connecting to the center of dend_0[0]. I did not specify which section was the soma. I just traced an image and exported the swc, never annotating any compartments. NEURON took the first section to be the soma and then connected later sections to its middle. The first section tu...
by DavidSwygart
Mon Apr 27, 2020 1:21 pm
Forum: Anatomically detailed models
Topic: morphology altered when Import3d exports to CellBuilder
Replies: 4
Views: 608

Re: morphology altered when Import3d exports to CellBuilder

I don't think it is purely a view rotation problem. Notice the location of the soma. It is the very wide portion below the dendrites in Import3d. The soma then moves above the dendrites in CellBuilder, while the rest of the axon seems to split off below the dendrites. I have rotated the images to be...
by DavidSwygart
Mon Apr 27, 2020 12:13 am
Forum: Anatomically detailed models
Topic: morphology altered when Import3d exports to CellBuilder
Replies: 4
Views: 608

morphology altered when Import3d exports to CellBuilder

I have loaded an swc with the Import3d GUI. The morphology looks correct. I then export the cell to CellBuilder GUI. At this point, the morphology looks incorrect. The longest branch containing the soma and axon seems to split, leaving the soma on one side of the dendrites and the axon on the other ...
by DavidSwygart
Wed Oct 09, 2019 9:36 am
Forum: Anatomically detailed models
Topic: 3D rotation in Cell Builder
Replies: 3
Views: 1893

Re: 3D rotation in Cell Builder

They should all belong to a single cell. Right now I am just modeling an axon terminal. I want to add a soma and dendrites.
by DavidSwygart
Fri Oct 04, 2019 5:37 pm
Forum: Anatomically detailed models
Topic: 3D rotation in Cell Builder
Replies: 3
Views: 1893

3D rotation in Cell Builder

Using "Import 3D", I imported a complicated branching structure of an axon terminal from a trace of an EM reconstruction. The EM reconstruction did not include the soma or dendrites of the cell. I now want to add a ball and stick representation of the soma and dendrites to my model. I am trying to u...
by DavidSwygart
Tue Jan 08, 2019 3:02 pm
Forum: Getting started
Topic: Connecting a new section to your model within a process or function
Replies: 1
Views: 1556

Connecting a new section to your model within a process or function

Hello, I am trying to add new sections to an existing model. I can create the new sections and successfully access the sections of the old model that I want to connect them to (using forsec), however, I get a syntax error when trying to connect them together. This only seems to occur while working w...
by DavidSwygart
Tue Dec 18, 2018 3:13 pm
Forum: Anatomically detailed models
Topic: Placing a point process at a known 3D location
Replies: 3
Views: 2085

Re: Placing a point process at a known 3D location

Thanks! I was thinking of doing something like this, but I just thought I would check because I often use way too many for loops to solve simple problems. I did implement the strategy you outlined and it worked great.
by DavidSwygart
Tue Dec 18, 2018 3:10 pm
Forum: The GUI
Topic: Broken Voltage Grapher
Replies: 3
Views: 2402

Re: Broken Voltage Grapher

Just an update for anyone reading this. I was creating a cell using custom code that read data from an SWC file. I switched to importing the SWC information using the import3D tool and everything is working now.
by DavidSwygart
Tue Dec 11, 2018 11:45 am
Forum: Anatomically detailed models
Topic: Placing a point process at a known 3D location
Replies: 3
Views: 2085

Placing a point process at a known 3D location

Using import3D I have created an anatomically detailed model of a cell from an SWC file. I now want to add synapses to this model. I know the 3D location of each synapse and have determined the 3D point from the SWC file that each synapse is closest to. Now, what is the best way to add these synapse...
by DavidSwygart
Wed Dec 05, 2018 12:33 pm
Forum: The GUI
Topic: Broken Voltage Grapher
Replies: 3
Views: 2402

Re: Broken Voltage Grapher

Hello, thanks for your quick response. I have sent the code that I have been having trouble with. I now notice that when I reduce nseg to a lower value, the grapher doesn't work even without specifying Ra. So, I am very confused as to what is going on.
by DavidSwygart
Wed Dec 05, 2018 1:17 am
Forum: The GUI
Topic: Broken Voltage Grapher
Replies: 3
Views: 2402

Broken Voltage Grapher

Hello, I am new to NEURON and am having problems using the GUI to plot voltage. I have created a script (SWC_read.hoc) to load SWC morphology data and add synapses at specific locations and also record voltage from output synapse locations. As I go along, I have been using the GUI to run the simulat...