diff --git a/replicabilitystamp/replicability_info.txt b/replicabilitystamp/replicability_info.txt new file mode 100644 index 0000000..3a37e33 --- /dev/null +++ b/replicabilitystamp/replicability_info.txt @@ -0,0 +1,8 @@ +Title: SynAnno: Interactive Guided Proofreading of Synaptic Annotations +Authors: Leander Lauenburg, Jakob Troidl, Adam Gohain, Zudi Lin, Hanspeter Pfister, Donglai Wei +Operating System: macOS 12.0+ (Monterey or later) +Repository: https://github.com/PytorchConnectomics/SynAnno +License: MIT +Setup: Docker-based; see setup_synanno.sh for install and run instructions +Interactive: Yes +Justification: SynAnno is an interactive proofreading tool designed for user-guided correction of synaptic annotations. Scripted reproduction is not feasible, as human interaction is essential for navigating neurons and validating synapses. A screen recording is provided to demonstrate the core functionality corresponding to the published demo. diff --git a/replicabilitystamp/screen_demo.mp4 b/replicabilitystamp/screen_demo.mp4 new file mode 100644 index 0000000..561fa2c Binary files /dev/null and b/replicabilitystamp/screen_demo.mp4 differ diff --git a/replicabilitystamp/setup_synanno.sh b/replicabilitystamp/setup_synanno.sh new file mode 100644 index 0000000..c2009e8 --- /dev/null +++ b/replicabilitystamp/setup_synanno.sh @@ -0,0 +1,55 @@ +#!/bin/bash + +APP_NAME="synanno-app" +CONTAINER_NAME="synanno-container" + +# Function to clone, build, and run the SynAnno application +function run_app() { + echo "Cloning and building SynAnno..." + if [ ! -d "SynAnno" ]; then + git clone https://github.com/PytorchConnectomics/SynAnno.git + fi + cd SynAnno || exit 1 + + echo "Building Docker image ($APP_NAME)..." + docker build -t "$APP_NAME" -f Dockerfile_uwsgi . + + echo "Running Docker container ($CONTAINER_NAME) on port 80..." + docker run -d --rm \ + -p 80:80 -p 9015:9015 \ + --name "$CONTAINER_NAME" \ + "$APP_NAME" + + sleep 5 + echo "Opening SynAnno in your browser at http://localhost/demo" + open http://localhost/demo 2>/dev/null || xdg-open http://localhost/demo +} + +# Function to stop and clean up the Docker container and image +function cleanup() { + echo "Stopping and removing Docker container (if running)..." + docker stop "$CONTAINER_NAME" 2>/dev/null || echo "Container not running." + + echo "Removing Docker image..." + docker rmi "$APP_NAME" +} + +# Handle command-line arguments +case "$1" in + "") + run_app + ;; + cleanup) + cleanup + ;; + help|-h|--help) + echo "Usage: bash setup_synanno.sh [cleanup]" + echo "" + echo " (no args) Set up and run SynAnno" + echo " cleanup Stop container and remove image" + ;; + *) + echo "Unknown argument: $1" + echo "Run with 'help' for usage." + ;; +esac diff --git a/doc/images/synanno_replicabilitystamp_img_250_250.png b/replicabilitystamp/synanno_replicabilitystamp_img_250_250.png similarity index 100% rename from doc/images/synanno_replicabilitystamp_img_250_250.png rename to replicabilitystamp/synanno_replicabilitystamp_img_250_250.png