Tools for editing SWC files (neuron morphology)

I have recently found myself having to pour over 100’s of reconstructions of neurons from http://NeuroMorpho.org and make small changes before I can analyze them further. I needed a free tool that could:

a) let me quickly preview the contents and
b) make changes to the SWC files (e.g. move some branches around, set/change node types, get rid of/merge short segments, etc…)

Finding such a tool has proven to be elusive. However a combination of them seems to be sufficient for the job. Below I go over the tools that were most helpful:

HBP Morphology Viewer: A quick, web-based SWC viewer

Pros: This tool is nice if you need to quickly view an SWC file and don’t want to install any software. You can upload your file and use the mouse to rotate the cell in 3D, use a side panel to show/hide different cell sections, and use buttons to save the file in a few formats (e.g. X3D and NeuroML). Default colors are not bad.

Cons: The camera controls are a bit clunky. It renders soma as a cylinder. You have to upload the SWC files, one at a time, to view them.

Cvapp (Standalone): A quick desktop SWC viewer

Screenshot.JPG

Pros: It’s a downloadable software that you could set up to open your SWC files by making it the default app for for the .SWC files. This makes it similar to image preview software, where it opens a 3D view of a SWC file once you click on it in a folder. You can use the mouse to rotate/zoom/pan the view, and UI controls to save the file in different formats and change how the cell is rendered.

Cons: It has to be installed. Requires Java. Soma is rendered as a rectangle(?).

OS: Windows, Linux, and Mac (?)

neuTube: desktop SWC editor

Pros: neuTube can view SWC files in 3D and allow editing of individual nodes. It has powerful node selection and manipulation features (see below screenshot). It is possible to change the rendering type (as spheres, cylinders, lines) and how the nodes are colored (see screenshot below). Can also change the color scheme and most other settings (by scrolling down and using “Advanced” button).

There is a powerful SWC cleanup type of feature (although says “Experimental”), that can be used to clean short nodes by deleting or merging them, as well as perform a few other manipulations (see screenshot below).

Cons: The default colors are a bit jarring. While you can change them, there does not appear to be a way to save this preference. Clunky save UI: After making SWC file edits you can press CTRL+S to save the file (overwrite). For “save as”, a .TIFF stack file must be open prior to opening the SWC file. To select a region you can press SHIFT+R, draw rectangle, then SHIFT+S to select the nodes under the rectangle.

There is also a “neuTu” project, which seems related, and looking at screenshots, possibly an updated version of “neuTube”. However, it requires >2GB of space — I did not test it.

OS: There are binaries for Windows and Mac. Might be possible to compile the source code on Linux (?).

Update:

By using neuTube, I’ve found various workarounds for the above issues.

Semi-persistent Settings: It is “sort of” possible retain settings in 3D view. Basically, the settings are saved as long as the 3D window is not closed, and you can use CTRL+S and the “Neurons” tab to save/open/close other SWC files.
First set your desired settings. Then, to view another SWC file using the same settings, in the top right panel “Neurons”, select the currently open file, press DEL to remove it from view. Then to open another SWC file, drag it from your folder onto the same Neuron tab.

Shortcut keys: While some menu items have keyboard shortcuts, many do not. However, you can use AutoHotKey (on Windows) to create macros and assign them to keyboard shortcuts. Here’s my AutoHotKey script for: Selecting the host branch of a node, change the type, set as root, select upstream, downstream.

Neuromantic: an older SWC editor, similar to neuTube

Pros: Can view and edit SWC files. Powerful node selection and manipulation features. A large array of pre-defined plots (see below).

Cons: The node editing interface is clunky – I had to refer to the manual a few times to make some simple changes. There doesn’t appear to be an easy way to change the z-coordinate (have to flip through stacks). Graphics look a bit dated. Windows only.

OS: Windows only.

I was able to do most of what I needed with neuTube. But Neuromantics might have a feature you need that complements neuTube.

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