Getting Started#

This guide gets a new user to a working SWC-Studio install and a first successful run.

Installation paths#

There are two supported ways to start:

  • use a packaged desktop release from GitHub Releases

  • install from source if you want the Python package, CLI, or a development setup

Supported Python versions#

Source installs currently support:

  • Python 3.10

  • Python 3.11

  • Python 3.12

Python 3.11 is the safest default for most users.

Packaged desktop release#

Use this path if you only need the desktop application:

  1. download the release archive for your platform

  2. extract it

  3. launch the included application

Release page:

Source install#

Clone the repository:

git clone <your-repo-url>
cd <repo-folder-name>

Conda#

conda create -n swc-studio python=3.11 -y
conda activate swc-studio
python -m pip install --upgrade pip
pip install -e ".[gui]"

venv on macOS or Linux#

python3 -m venv .venv
source .venv/bin/activate
python -m pip install --upgrade pip
pip install -e ".[gui]"

venv on Windows PowerShell#

py -m venv .venv
.\.venv\Scripts\Activate.ps1
python -m pip install --upgrade pip
pip install -e ".[gui]"

CLI-only install#

python -m pip install -e .

Verify installation#

For a source install:

swcstudio --help
swcstudio-gui --help

If the console script is not on your path, use module mode:

python -m swcstudio.cli.cli --help
python -m swcstudio.gui.main

First CLI checks#

Start with a read-only inspection command:

swcstudio check ./data/single-soma.swc
swcstudio validate ./data/single-soma.swc

Then try an edit command:

swcstudio auto-label ./data/single-soma.swc
swcstudio set-type ./data/single-soma.swc --node-id 14169 --new-type 3
swcstudio simplify ./data/single-soma.swc
swcstudio connect ./data/single-soma.swc --start-id 10 --end-id 22

Single-file edit commands write both the updated SWC and the matching log into the source file’s default output directory. No separate --write flag is required.

First GUI checks#

Launch the GUI:

swcstudio-gui

Then:

  1. open an SWC file

  2. review the automatically generated issue list

  3. select an issue and let the app route you to the matching repair tool

  4. save or close the file to write the session log and saved copy

Default outputs#

For a source file:

  • <folder>/<stem>.swc

the default single-file output directory is:

  • <folder>/<stem>_swc_studio_output/

Typical files written there include:

  • validation reports

  • edited SWC copies

  • per-operation logs

  • GUI session logs

  • GUI saved copies