diff --git a/.gitignore b/.gitignore
index 74c2474..ac1261b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -31,7 +31,6 @@ pytorch_connectomics/
.coverage
coverage.xml
dist/
-.env
-.env.*
+
*.log
.github/workflows/docker-test.yml
diff --git a/COPILOT.md b/COPILOT.md
new file mode 100644
index 0000000..f8cdfc1
--- /dev/null
+++ b/COPILOT.md
@@ -0,0 +1,86 @@
+**Project Summary**
+- **Name:** pytc-client — Desktop client and services for Pytorch Connectomics
+- **Purpose:** Electron + React desktop client that interacts with FastAPI backend services and the `pytorch_connectomics` library for connectomics workflows.
+
+**Top-level Structure**
+- **`client/`**: Electron + React frontend (CRA). Important files:
+ - `client/package.json` — frontend scripts (`start`, `build`, `electron`).
+ - `client/main.js` — Electron entrypoint.
+ - `client/src/` — React source; components in `client/src/components/`.
+- **`server_api/`**: FastAPI application (API server)
+ - `server_api/main.py` — API entrypoint.
+ - `server_api/requirements.txt` — Python deps for API.
+- **`server_pytc/`**: PyTC worker service used for model inference or background tasks
+ - `server_pytc/main.py` — worker entrypoint.
+- **`pytorch_connectomics/`**: Library (local package) with models, configs, and utilities used by the worker.
+ - `pytorch_connectomics/setup.py` — library install entry.
+ - `pytorch_connectomics/configs/` — example YAML config files.
+- **`docker/`**: Docker resources for containerized backend; root `docker-compose.yaml` / `Dockerfile` exist.
+- **`scripts/`**: Helper scripts
+ - `scripts/bootstrap.sh` / `scripts/bootstrap.ps1` — one-time install/bootstrap
+ - `start.sh` / `start.bat` — start the full stack (servers + Electron client)
+- **`docs/`, `notebooks/`, `tests/`**: documentation, Jupyter notebooks, and unit tests respectively.
+
+**Important Root Files**
+- `package.json` (root): convenience npm scripts added to operate on the `client/` folder from repository root.
+- `README.md`: project setup and running instructions.
+
+**Common Developer Commands**
+- Bootstrap (one-time):
+```bash
+./scripts/bootstrap.sh # macOS / Linux
+scripts\bootstrap.ps1 # Windows PowerShell
+```
+- Start full stack (desktop + services):
+```bash
+./start.sh # macOS / Linux
+start.bat # Windows CMD
+```
+- Build frontend from repo root (convenience scripts added):
+```bash
+npm run client:install # install dependencies inside `client/`
+npm run client:build # build production frontend in `client/build`
+npm run client:dev # run frontend dev server (react-scripts start)
+npm run client:electron # run Electron (`electron .`) from `client/`
+```
+- Manual backend run (dev):
+```bash
+python -m venv .venv
+# activate venv
+source .venv/bin/activate # macOS / Linux
+.\.venv\Scripts\activate # Windows PowerShell
+pip install -r server_api/requirements.txt
+python server_api/main.py
+python server_pytc/main.py
+```
+- Tests:
+```bash
+pytest -q
+```
+- Docker backend (build & run):
+```bash
+docker compose build backend
+docker compose up backend
+docker compose down
+```
+
+**Where to Make Changes**
+- Frontend UI / components: edit `client/src/` and update `client/package.json` scripts as needed.
+- Electron behavior: edit `client/main.js` and electron-specific code.
+- API endpoints & backend logic: edit `server_api/` (FastAPI) and `server_pytc/` for worker behavior.
+- Models/configs: `pytorch_connectomics/` contains models, configs, and experiment YAMLs.
+
+**CI / Automation Tips**
+- CI jobs can call `npm --prefix client run build` (same as `npm run client:build`) to build frontend from repo root.
+- For parallel dev workflows (backend + frontend concurrently), consider adding `concurrently` or `npm-run-all` as dev dependencies and a `dev` script in root.
+
+**Notes & Recommendations**
+- Root `package.json` now includes `client:*` convenience scripts that use `npm --prefix client` to be cross-platform.
+- `client/package.json` uses `react-scripts` and defines `build` and `electron` scripts; keep those in sync when modifying frontend tooling.
+- Use `start.sh` / `start.bat` for the supported, repository-provided startup flow when possible.
+
+**Contact / Reference**
+- See `README.md` for more detailed setup and video demo link.
+- Use `tests/` for examples of expected behavior and for regression checks.
+
+(Generated by Copilot assistant for developer reference.)
\ No newline at end of file
diff --git a/DEVLOG.md b/DEVLOG.md
new file mode 100644
index 0000000..02ae7d0
--- /dev/null
+++ b/DEVLOG.md
@@ -0,0 +1,95 @@
+# DEVLOG.md — pytc-client Development Log
+
+This file records the major development steps, design decisions, and UI/UX changes made to the pytc-client project. It is formatted for easy reading by humans and AI agents.
+
+---
+
+## Project Context
+- **Repo:** PytorchConnectomics/pytc-client
+- **Frontend:** React + Electron (Ant Design)
+- **Backend:** FastAPI (Python), local user management for prototype
+
+---
+
+## Major Features & Changes
+
+### [2025-11-21] Backend User Management
+* **Backend Auth**: Integrated FastAPI with `python-jose` (JWT) and `passlib` (bcrypt) for secure authentication.
+* **Database**: Added SQLite database (`sql_app.db`) with SQLAlchemy models for Users.
+* **Frontend Integration**: Updated `UserContext` to communicate with backend endpoints (`/register`, `/token`, `/users/me`) instead of local storage.
+* **Dependencies**: Added `python-jose`, `passlib`, `sqlalchemy` to requirements.
+
+### [2025-11-21] Advanced File Management & UI Polish
+* **Manual Sign Out**: Added a sign-out button to the header, allowing users to return to the Welcome screen.
+* **File Previews**: Implemented a preview modal for files (images and text) triggered by double-click or context menu.
+* **Multi-Select & Drag Selection**: Added drag selection box and keyboard shortcuts (Ctrl/Shift) for selecting multiple files.
+* **Enhanced Drag & Drop**: Enabled moving multiple selected files/folders at once, including within the same parent directory.
+* **Context Menu Enhancements**: Updated context menu to handle multiple selections (bulk Copy/Delete) and hide "Preview" for multi-select.
+* **Bug Fixes**: Resolved issues with drag selection (single item) and Electron path handling on Windows.
+
+### 1. Welcome Page
+- Added a full-screen Welcome page as the app's entry point.
+- Includes project name, intro, and warm message.
+- Two buttons: "Sign in" and "Sign up".
+- Styled to resemble cursor.com (modern, clean, gradient background).
+- Welcome page is always shown on app start (automatic sign out).
+
+### 2. Backend User Management (New)
+- Replaced local storage with production-ready backend auth.
+- Users are stored in `server_api/sql_app.db` (SQLite).
+- Passwords are hashed with bcrypt.
+- JWT tokens used for session management (stored in localStorage).
+
+### 3. Main App Navigation
+- After login, user sees main app view (tabs: Visualization, Model Training, Model Inference, Tensorboard, Files).
+- "Welcome" tab removed from main menu after login.
+- Navigation to Welcome page is blocked after login.
+
+### 4. Files Tab (Google Drive-like)
+- Files tab shows three file slots per user.
+- Each slot displays file info (name, size, type) or "Empty".
+- Upload, rename, and delete actions for each slot (Ant Design components).
+- Upload is local only; rename uses modal; delete clears slot.
+
+### 5. Debugging & Build Process
+- Debug banners/messages added and removed for troubleshooting.
+- Reminder: Electron app uses static build (`client/build/`), so `npm run build` is required after code changes.
+- Hot reload only works in browser dev mode (`npm start`).
+
+---
+
+## Known Issues & Fixes
+- [x] Welcome page not showing: fixed by auto sign out on app start.
+- [x] "Welcome" tab visible after login: removed from menu.
+- [x] Debug messages visible: removed.
+- [x] Modals not working in Electron: fixed after proper build/restart.
+- [x] Drag selection not selecting single items: fixed.
+- [x] Electron "ERR_FILE_NOT_FOUND": fixed path separator in main.js.
+
+---
+
+## Next Steps / TODOs
+- [x] Add multi-file support or previews in Files tab.
+- [x] Add manual sign-out button in main app view.
+- [x] Integrate backend user management (FastAPI, JWT, etc.) for production.
+- [ ] Add user profile editing and avatar upload.
+- [ ] Improve file upload to support actual file storage (not just metadata).
+
+---
+
+## How to Develop & Test
+- Make code changes in `client/src/`.
+- Run `npm --prefix client run build` to update the Electron app.
+- Start the app with `./start.bat`.
+- For live development, use `npm start` (browser only).
+
+---
+
+## AI Agent Notes
+- All major UI/UX changes, context, and user flows are documented here.
+- Use this file to bootstrap further development, onboarding, or automation.
+- For backend integration, see FastAPI endpoints and user model notes above.
+
+---
+
+_Last updated: 2025-11-21_
diff --git a/bash.exe.stackdump b/bash.exe.stackdump
new file mode 100644
index 0000000..e7b5590
--- /dev/null
+++ b/bash.exe.stackdump
@@ -0,0 +1,29 @@
+Stack trace:
+Frame Function Args
+0007FFFFBBB0 00021006118E (00021028DEE8, 000210272B3E, 0007FFFFBBB0, 0007FFFFAAB0) msys-2.0.dll+0x2118E
+0007FFFFBBB0 0002100469BA (000000000000, 000000000000, 000000000000, 0007FFFFBE88) msys-2.0.dll+0x69BA
+0007FFFFBBB0 0002100469F2 (00021028DF99, 0007FFFFBA68, 0007FFFFBBB0, 000000000000) msys-2.0.dll+0x69F2
+0007FFFFBBB0 00021006A41E (000000000000, 000000000000, 000000000000, 000000000000) msys-2.0.dll+0x2A41E
+0007FFFFBBB0 00021006A545 (0007FFFFBBC0, 000000000000, 000000000000, 000000000000) msys-2.0.dll+0x2A545
+0007FFFFBE90 00021006B9A5 (0007FFFFBBC0, 000000000000, 000000000000, 000000000000) msys-2.0.dll+0x2B9A5
+End of stack trace
+Loaded modules:
+000100400000 bash.exe
+7FFA3F430000 ntdll.dll
+7FFA3E6F0000 KERNEL32.DLL
+7FFA3CF90000 KERNELBASE.dll
+7FFA3EDD0000 USER32.dll
+7FFA3D290000 win32u.dll
+000210040000 msys-2.0.dll
+7FFA3D510000 GDI32.dll
+7FFA3CE70000 gdi32full.dll
+7FFA3CAC0000 msvcp_win.dll
+7FFA3CB60000 ucrtbase.dll
+7FFA3D450000 advapi32.dll
+7FFA3D8B0000 msvcrt.dll
+7FFA3D730000 sechost.dll
+7FFA3E4E0000 RPCRT4.dll
+7FFA3CE40000 bcrypt.dll
+7FFA3C2A0000 CRYPTBASE.DLL
+7FFA3D370000 bcryptPrimitives.dll
+7FFA3EC80000 IMM32.DLL
diff --git a/client/.env b/client/.env
index e92841b..9db1133 100644
--- a/client/.env
+++ b/client/.env
@@ -1,2 +1,4 @@
-REACT_APP_API_PROTOCOL=http
-REACT_APP_API_URL=localhost:4242
+SKIP_PREFLIGHT_CHECK=true
+REACT_APP_SERVER_PROTOCOL=http
+REACT_APP_SERVER_URL=localhost:4242
+PORT=3001
diff --git a/client/main.js b/client/main.js
index e3bfae7..a42a4c1 100644
--- a/client/main.js
+++ b/client/main.js
@@ -7,18 +7,20 @@ require('electron-reload')(__dirname, {
let mainWindow
-function createWindow () {
+function createWindow() {
mainWindow = new BrowserWindow({
width: 800,
height: 600,
webPreferences: {
nodeIntegration: true,
- contextIsolation: false
+ contextIsolation: false,
+ webSecurity: false, // Allow loading iframes from localhost
+ allowRunningInsecureContent: true
}
})
mainWindow.loadURL(url.format({
- pathname: path.join(__dirname, './build/index.html'),
+ pathname: path.join(__dirname, 'build', 'index.html'),
protocol: 'file:',
slashes: true
}))
diff --git a/client/package-lock.json b/client/package-lock.json
index dd9df65..cfd80fa 100644
--- a/client/package-lock.json
+++ b/client/package-lock.json
@@ -30,6 +30,7 @@
},
"devDependencies": {
"@babel/plugin-proposal-private-property-in-object": "^7.16.7",
+ "babel-loader": "8.2.2",
"cross-env": "^7.0.3",
"electron-reload": "^2.0.0-alpha.1",
"prettier": "^3.3.2"
@@ -5704,12 +5705,14 @@
}
},
"node_modules/babel-loader": {
- "version": "8.3.0",
- "resolved": "https://registry.npmjs.org/babel-loader/-/babel-loader-8.3.0.tgz",
- "integrity": "sha512-H8SvsMF+m9t15HNLMipppzkC+Y2Yq+v3SonZyU70RBL/h1gxPkH08Ot8pEE9Z4Kd+czyWJClmFS8qzIP9OZ04Q==",
+ "version": "8.2.2",
+ "resolved": "https://registry.npmjs.org/babel-loader/-/babel-loader-8.2.2.tgz",
+ "integrity": "sha512-JvTd0/D889PQBtUXJ2PXaKU/pjZDMtHA9V2ecm+eNRmmBCMR09a+fmpGTNwnJtFmFl5Ei7Vy47LjBb+L0wQ99g==",
+ "dev": true,
+ "license": "MIT",
"dependencies": {
"find-cache-dir": "^3.3.1",
- "loader-utils": "^2.0.0",
+ "loader-utils": "^1.4.0",
"make-dir": "^3.1.0",
"schema-utils": "^2.6.5"
},
@@ -5721,10 +5724,39 @@
"webpack": ">=2"
}
},
+ "node_modules/babel-loader/node_modules/json5": {
+ "version": "1.0.2",
+ "resolved": "https://registry.npmjs.org/json5/-/json5-1.0.2.tgz",
+ "integrity": "sha512-g1MWMLBiz8FKi1e4w0UyVL3w+iJceWAFBAaBnnGKOpNa5f8TLktkbre1+s6oICydWAm+HRUGTmI+//xv2hvXYA==",
+ "dev": true,
+ "license": "MIT",
+ "dependencies": {
+ "minimist": "^1.2.0"
+ },
+ "bin": {
+ "json5": "lib/cli.js"
+ }
+ },
+ "node_modules/babel-loader/node_modules/loader-utils": {
+ "version": "1.4.2",
+ "resolved": "https://registry.npmjs.org/loader-utils/-/loader-utils-1.4.2.tgz",
+ "integrity": "sha512-I5d00Pd/jwMD2QCduo657+YM/6L3KZu++pmX9VFncxaxvHcru9jx1lBaFft+r4Mt2jK0Yhp41XlRAihzPxHNCg==",
+ "dev": true,
+ "license": "MIT",
+ "dependencies": {
+ "big.js": "^5.2.2",
+ "emojis-list": "^3.0.0",
+ "json5": "^1.0.1"
+ },
+ "engines": {
+ "node": ">=4.0.0"
+ }
+ },
"node_modules/babel-loader/node_modules/schema-utils": {
"version": "2.7.1",
"resolved": "https://registry.npmjs.org/schema-utils/-/schema-utils-2.7.1.tgz",
"integrity": "sha512-SHiNtMOUGWBQJwzISiVYKu82GiV4QYGePp3odlY1tuKO7gPtphAT5R/py0fA6xtbgLL/RvtJZnU9b8s0F1q0Xg==",
+ "dev": true,
"dependencies": {
"@types/json-schema": "^7.0.5",
"ajv": "^6.12.4",
@@ -6286,9 +6318,9 @@
}
},
"node_modules/caniuse-lite": {
- "version": "1.0.30001643",
- "resolved": "https://registry.npmjs.org/caniuse-lite/-/caniuse-lite-1.0.30001643.tgz",
- "integrity": "sha512-ERgWGNleEilSrHM6iUz/zJNSQTP8Mr21wDWpdgvRwcTXGAq6jMtOUPP4dqFPTdKqZ2wKTdtB+uucZ3MRpAUSmg==",
+ "version": "1.0.30001756",
+ "resolved": "https://registry.npmjs.org/caniuse-lite/-/caniuse-lite-1.0.30001756.tgz",
+ "integrity": "sha512-4HnCNKbMLkLdhJz3TToeVWHSnfJvPaq6vu/eRP0Ahub/07n484XHhBF5AJoSGHdVrS8tKFauUQz8Bp9P7LVx7A==",
"funding": [
{
"type": "opencollective",
@@ -6302,7 +6334,8 @@
"type": "github",
"url": "https://github.com/sponsors/ai"
}
- ]
+ ],
+ "license": "CC-BY-4.0"
},
"node_modules/case-sensitive-paths-webpack-plugin": {
"version": "2.4.0",
@@ -17360,6 +17393,25 @@
}
}
},
+ "node_modules/react-scripts/node_modules/babel-loader": {
+ "version": "8.4.1",
+ "resolved": "https://registry.npmjs.org/babel-loader/-/babel-loader-8.4.1.tgz",
+ "integrity": "sha512-nXzRChX+Z1GoE6yWavBQg6jDslyFF3SDjl2paADuoQtQW10JqShJt62R6eJQ5m/pjJFDT8xgKIWSP85OY8eXeA==",
+ "license": "MIT",
+ "dependencies": {
+ "find-cache-dir": "^3.3.1",
+ "loader-utils": "^2.0.4",
+ "make-dir": "^3.1.0",
+ "schema-utils": "^2.6.5"
+ },
+ "engines": {
+ "node": ">= 8.9"
+ },
+ "peerDependencies": {
+ "@babel/core": "^7.0.0",
+ "webpack": ">=2"
+ }
+ },
"node_modules/react-scripts/node_modules/fs-extra": {
"version": "10.1.0",
"resolved": "https://registry.npmjs.org/fs-extra/-/fs-extra-10.1.0.tgz",
@@ -17384,6 +17436,24 @@
"graceful-fs": "^4.1.6"
}
},
+ "node_modules/react-scripts/node_modules/schema-utils": {
+ "version": "2.7.1",
+ "resolved": "https://registry.npmjs.org/schema-utils/-/schema-utils-2.7.1.tgz",
+ "integrity": "sha512-SHiNtMOUGWBQJwzISiVYKu82GiV4QYGePp3odlY1tuKO7gPtphAT5R/py0fA6xtbgLL/RvtJZnU9b8s0F1q0Xg==",
+ "license": "MIT",
+ "dependencies": {
+ "@types/json-schema": "^7.0.5",
+ "ajv": "^6.12.4",
+ "ajv-keywords": "^3.5.2"
+ },
+ "engines": {
+ "node": ">= 8.9.0"
+ },
+ "funding": {
+ "type": "opencollective",
+ "url": "https://opencollective.com/webpack"
+ }
+ },
"node_modules/react-scripts/node_modules/semver": {
"version": "7.6.3",
"resolved": "https://registry.npmjs.org/semver/-/semver-7.6.3.tgz",
diff --git a/client/package.json b/client/package.json
index dbe998a..71742ff 100644
--- a/client/package.json
+++ b/client/package.json
@@ -52,6 +52,7 @@
},
"devDependencies": {
"@babel/plugin-proposal-private-property-in-object": "^7.16.7",
+ "babel-loader": "8.2.2",
"cross-env": "^7.0.3",
"electron-reload": "^2.0.0-alpha.1",
"prettier": "^3.3.2"
@@ -60,6 +61,6 @@
"nth-check": "$nth-check",
"resolve-url-loader": "^5.0.0",
"svgo": "^3.3.2",
- "webpack-dev-server": "^5.2.1"
+ "webpack-dev-server": "^4.15.0"
}
-}
+}
\ No newline at end of file
diff --git a/client/src/App.js b/client/src/App.js
index 9e605b8..26e308e 100644
--- a/client/src/App.js
+++ b/client/src/App.js
@@ -1,7 +1,9 @@
import { useContext, useEffect, useState } from 'react'
import './App.css'
import Views from './views/Views'
+import Welcome from './views/Welcome'
import { AppContext, ContextWrapper } from './contexts/GlobalContext'
+import UserContextWrapper, { UserContext } from './contexts/UserContext'
import { YamlContextWrapper } from './contexts/YamlContext'
function CacheBootstrapper ({ children }) {
@@ -30,17 +32,24 @@ function CacheBootstrapper ({ children }) {
return children
}
+function MainContent () {
+ const { currentUser } = useContext(UserContext)
+ return currentUser ?
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
)
}
diff --git a/client/src/components/NeuroglancerViewer.js b/client/src/components/NeuroglancerViewer.js
new file mode 100644
index 0000000..44d6dd4
--- /dev/null
+++ b/client/src/components/NeuroglancerViewer.js
@@ -0,0 +1,150 @@
+import React, { useState, useEffect } from 'react';
+import { Button, Spin, Alert, Typography } from 'antd';
+import { ReloadOutlined } from '@ant-design/icons';
+import axios from 'axios';
+
+const { Text, Title } = Typography;
+const API_BASE = `${process.env.REACT_APP_SERVER_PROTOCOL || 'http'}://${process.env.REACT_APP_SERVER_URL || 'localhost:4243'}`;
+
+/**
+ * NeuroglancerViewer Component
+ *
+ * Loads and displays Neuroglancer viewer in an iframe using the project's image files.
+ * Uses the same approach as the Visualization tab.
+ *
+ * @param {number} projectId - Project ID to load viewer for
+ * @param {object} currentSynapse - Current synapse for position reference
+ */
+function NeuroglancerViewer({ projectId = 1, currentSynapse }) {
+ const [viewerUrl, setViewerUrl] = useState(null);
+ const [loading, setLoading] = useState(true);
+ const [error, setError] = useState(null);
+
+ // Load Neuroglancer viewer on mount
+ useEffect(() => {
+ loadViewer();
+ }, [projectId]);
+
+ const loadViewer = async () => {
+ setLoading(true);
+ setError(null);
+
+ try {
+ const response = await axios.get(
+ `${API_BASE}/api/synanno/ng-url/${projectId}`,
+ { withCredentials: true }
+ );
+
+ if (response.data.url) {
+ setViewerUrl(response.data.url);
+ } else {
+ // If backend returns a message instead of URL (transition state)
+ if (response.data.message) {
+ // We can handle the message here, but for now let's just show the "Setup in Progress" state
+ // by not setting the URL.
+ console.log("Neuroglancer message:", response.data.message);
+ }
+ setError(null); // Clear error if it's just a transition message
+ }
+ } catch (err) {
+ console.error('Failed to load Neuroglancer viewer', err);
+ setError(err.response?.data?.detail || 'Failed to load Neuroglancer viewer');
+ } finally {
+ setLoading(false);
+ }
+ };
+
+ const refreshViewer = () => {
+ loadViewer();
+ };
+
+ if (loading) {
+ return (
+
+
+ );
+ }
+
+ if (error) {
+ return (
+
+ );
+ }
+
+ // Display viewer in iframe
+ return (
+
+
+
+ Synapse #{currentSynapse.id}
+
+ )}
+
+ {viewerUrl ? (
+
+ ) : (
+
+
Setup in Progress
+
Data server is running. Preparing viewer...
+
+
+ )}
+
+ No synapse selected
+
+ );
+ }
+
+ return (
+
+ {/* Current Synapse Info */}
+
+
Synapse #{currentSynapse.id}
+
+
+ Position: ({currentSynapse.x.toFixed(1)}, {currentSynapse.y.toFixed(1)}, {currentSynapse.z.toFixed(1)})
+
+ {currentSynapse.confidence && (
+
+ Confidence: {(currentSynapse.confidence * 100).toFixed(0)}%
+
+ )}
+
+
+
+
+
+ {/* Status Classification */}
+
+ Status Classification
+
+
+
+
+
+
+ {/* Neuron ID Inputs */}
+
+ Pre-synaptic Neuron ID
+
+
+
+ Post-synaptic Neuron ID
+
+
+
+
+ {/* Action Buttons */}
+
+
+ Save (S)
+
+
+
+ {/* Progress Section */}
+
+
Progress
+
+
+ {reviewedCount} / {totalErrors} reviewed
+
+
+
+ {/* Synapse List */}
+
(
+ onSelectSynapse(index)}
+ style={{
+ cursor: 'pointer',
+ backgroundColor: index === currentIndex ? '#e6f7ff' : 'transparent',
+ borderLeft: index === currentIndex ? '3px solid #1890ff' : '3px solid transparent',
+ padding: '8px 12px',
+ transition: 'all 0.2s'
+ }}
+ onMouseEnter={(e) => {
+ if (index !== currentIndex) {
+ e.currentTarget.style.backgroundColor = '#f5f5f5';
+ }
+ }}
+ onMouseLeave={(e) => {
+ if (index !== currentIndex) {
+ e.currentTarget.style.backgroundColor = 'transparent';
+ }
+ }}
+ >
+
+
+ Synapse #{synapse.id}
+ {getStatusIcon(synapse.status)}
+
+
+ ({synapse.x.toFixed(1)}, {synapse.y.toFixed(1)}, {synapse.z.toFixed(1)})
+
+ {synapse.confidence && (
+
+ Confidence: {(synapse.confidence * 100).toFixed(0)}%
+
+ )}
+
+ )}
+ />
+
+ {children}
+
+ );
+};
+
+export default UserContextWrapper;
diff --git a/client/src/views/Files.js b/client/src/views/Files.js
new file mode 100644
index 0000000..1c44a0c
--- /dev/null
+++ b/client/src/views/Files.js
@@ -0,0 +1,11 @@
+import React from 'react';
+import FilesManager from './FilesManager';
+
+export default function Files() {
+ return (
+
+
Files
+ (itemRefs.current[item.key] = el)}
+ draggable={!isEditing}
+ onDragStart={(e) => handleDragStart(e, item.key, type)}
+ onDragOver={type === 'folder' ? handleDragOver : undefined}
+ onDrop={type === 'folder' ? (e) => handleDrop(e, item.key) : undefined}
+ onContextMenu={(e) => handleContextMenu(e, 'item', item.key)}
+ onClick={(e) => {
+ e.stopPropagation();
+ if (e.ctrlKey) {
+ setSelectedItems((prev) => (isSelected ? prev.filter((k) => k !== item.key) : [...prev, item.key]));
+ } else if (e.shiftKey && selectedItems.length) {
+ setSelectedItems((prev) => [...prev, item.key]);
+ } else {
+ setSelectedItems([item.key]);
+ }
+ }}
+ onDoubleClick={() => {
+ if (isEditing) return;
+ if (type === 'folder') handleNavigate(item.key);
+ else handlePreview(item.key);
+ }}
+ style={{
+ width: viewMode === 'grid' ? 100 : '100%',
+ padding: 8,
+ margin: viewMode === 'grid' ? 8 : 0,
+ textAlign: viewMode === 'grid' ? 'center' : 'left',
+ cursor: 'pointer',
+ borderRadius: 4,
+ backgroundColor: isSelected ? '#e6f7ff' : 'transparent',
+ border: isSelected ? '1px solid #1890ff' : '1px solid transparent',
+ display: viewMode === 'list' ? 'flex' : 'block',
+ alignItems: 'center',
+ userSelect: 'none',
+ }}
+ >
+
+ {React.cloneElement(icon, { style: { fontSize: viewMode === 'grid' ? 48 : 24, color: type === 'folder' ? '#1890ff' : '#555' } })}
+
+ {isEditing ? (
+
setTempName(e.target.value)}
+ onBlur={() => (newItemType ? finishCreateFolder() : finishRename())}
+ onClick={(e) => e.stopPropagation()}
+ onKeyDown={(e) => e.stopPropagation()}
+ style={{ width: viewMode === 'grid' ? '100%' : 300 }}
+ />
+ ) : (
+
{item.title || item.name}
+ )}
+
+
+
+
setTempName(e.target.value)}
+ onBlur={finishCreateFolder}
+ onClick={(e) => e.stopPropagation()}
+ onKeyDown={(e) => e.stopPropagation()}
+ style={{ width: viewMode === 'grid' ? '100%' : 300 }}
+ />
+
{
+ if (isDragSelecting.current) {
+ isDragSelecting.current = false;
+ return;
+ }
+ setSelectedItems([]);
+ setContextMenu(null);
+ }}
+ onContextMenu={(e) => handleContextMenu(e, 'container')}
+ >
+ {/* Toolbar & Breadcrumbs */}
+
+
} onClick={handleUp} disabled={currentFolder === 'root'} size="small" />
+
+ {getBreadcrumbs().map((f) => (
+ handleNavigate(f.key)} style={{ cursor: 'pointer' }}>
+ {f.key === 'root' ?
+ ))}
+
+
:
}
+ onClick={() => setViewMode(viewMode === 'grid' ? 'list' : 'grid')}
+ title={viewMode === 'grid' ? 'Switch to List View' : 'Switch to Grid View'}
+ />
+
+
+ {/* Content Area */}
+
handleDrop(e, currentFolder)}
+ >
+ {currentFolders.length === 0 && currentFiles.length === 0 && !newItemType && (
+
+
+ )}
+ {currentFolders.map((f) => renderItem(f, 'folder'))}
+ {renderNewFolderPlaceholder()}
+ {currentFiles.map((f) => renderItem(f, 'file'))}
+ {selectionBox && (
+
+ )}
+
+
+ {/* Context Menu */}
+ {contextMenu && (
+
+
{
+ setContextMenu(null);
+ if (key === 'new_folder') startCreateFolder();
+ if (key === 'upload') handleUploadClick();
+ if (key === 'rename') {
+ const item = folders.find((f) => f.key === contextMenu.key) || (files[currentFolder] || []).find((f) => f.key === contextMenu.key);
+ startRename(contextMenu.key, item.title || item.name);
+ }
+ if (key === 'copy') handleCopy(selectedItems.length > 0 ? selectedItems : [contextMenu.key]);
+ if (key === 'delete') handleDelete(selectedItems.length > 0 ? selectedItems : [contextMenu.key]);
+ if (key === 'preview') handlePreview(contextMenu.key);
+ if (key === 'properties') handleProperties(selectedItems.length > 0 ? selectedItems : [contextMenu.key]);
+ }}
+ items={getContextMenuItems()}
+ />
+
+ )}
+
+ {/* Preview Modal */}
+
setPreviewFile(null)}
+ footer={null}
+ width={800}
+ >
+ {previewFile && (
+
+ {previewFile.type?.startsWith('image') ? (
+
+ ) : (
+
+
{previewFile.name === 'readme.txt' ? "This is a dummy text file content.\n\nIn a real app, this would fetch the file content from the server." : "Preview not available for this file type."}
+
+ )}
+
+
+ {/* Properties Modal */}
+
setPropertiesData(null)}
+ footer={[
+ setPropertiesData(null)}>
+ Close
+ ,
+ ]}
+ width={500}
+ >
+ {propertiesData && propertiesData.type === 'single' && (
+
+
+ {propertiesData.isFolder ? (
+
+ ) : (
+
+ )}
+
+
{propertiesData.name}
+
{propertiesData.isFolder ? 'Folder' : 'File'}
+
+
+
+
+ Type:
+ {propertiesData.fileType}
+
+
+ Size:
+ {propertiesData.size}
+
+
+ Created:
+ {propertiesData.created}
+
+
+ Modified:
+ {propertiesData.modified}
+
+
+
+
Selection Summary
+
+
+ Total Items:
+ {propertiesData.totalCount}
+
+
+ Folders:
+ {propertiesData.folderCount}
+
+
+ Files:
+ {propertiesData.fileCount}
+
+
+ Total Size:
+ {propertiesData.totalSize}
+
+
+
+
+
+ );
+ }
+
+ // Empty state
+ if (synapses.length === 0) {
+ return (
+
+
+ );
+ }
+
+ return (
+
+ {/* Left Panel: Synapse List */}
+
+
+
+ {/* Center: Neuroglancer Viewer */}
+
+
+
+ {/* Right Panel: Proofreading Controls */}
+
+
+
+ );
+}
+
+export default ProofReading;
diff --git a/client/src/views/Views.js b/client/src/views/Views.js
index c77ae9c..1feeca3 100644
--- a/client/src/views/Views.js
+++ b/client/src/views/Views.js
@@ -1,150 +1,49 @@
-import React, { useState, useEffect } from 'react'
-import DataLoader from './DataLoader'
-import Visualization from '../views/Visualization'
-import ModelTraining from '../views/ModelTraining'
-import ModelInference from '../views/ModelInference'
-import Monitoring from '../views/Monitoring'
-import Chatbot from '../components/Chatbot'
-import { Layout, Menu, Button } from 'antd'
-import { MessageOutlined } from '@ant-design/icons'
-import { getNeuroglancerViewer } from '../utils/api'
+import React, { useState, useContext } from 'react'
+import { Layout, Menu, Avatar, Typography, Space, Button, Tooltip } from 'antd'
+import { FolderOpenOutlined, DesktopOutlined, UserOutlined, LogoutOutlined } from '@ant-design/icons'
+import FilesManager from './FilesManager'
+import Workspace from './Workspace'
+import { UserContext } from '../contexts/UserContext'
-const { Content, Sider } = Layout
+const { Content } = Layout
+const { Text } = Typography
-function Views () {
- const [current, setCurrent] = useState('visualization')
- const [viewers, setViewers] = useState([])
- const [isLoading, setIsLoading] = useState(false)
- const [isInferring, setIsInferring] = useState(false)
- const [isChatOpen, setIsChatOpen] = useState(false)
- console.log(viewers)
-
- const onClick = (e) => {
- setCurrent(e.key)
- }
+function Views() {
+ const [current, setCurrent] = useState('files')
+ const { currentUser, autoSignOut } = useContext(UserContext)
const items = [
- { label: 'Visualization', key: 'visualization' },
- { label: 'Model Training', key: 'training' },
- { label: 'Model Inference', key: 'inference' },
- { label: 'Tensorboard', key: 'monitoring' }
+ { label: 'File Management', key: 'files', icon:
- {isLoading
- ? (Loading the viewer ...
)
- : (
- <>
- setCollapsed(value)}
- theme='light'
- collapsedWidth='0'
- >
-
-
-
-
-
- {isChatOpen ? (
-
- setIsChatOpen(false)} />
-
- ) : (
-
+
+
+
+
+ {currentUser ? currentUser.name : 'Guest'}
+
+
+
+
+
+ {current === 'files' ?
)
}
diff --git a/client/src/views/Welcome.js b/client/src/views/Welcome.js
new file mode 100644
index 0000000..5970858
--- /dev/null
+++ b/client/src/views/Welcome.js
@@ -0,0 +1,177 @@
+import React, { useState, useContext, useEffect } from 'react';
+import { Card, Button, Input, Modal, Typography, message, Space } from 'antd';
+import { UserOutlined, LockOutlined, RocketOutlined } from '@ant-design/icons';
+import { UserContext } from '../contexts/UserContext';
+
+const { Title, Text } = Typography;
+
+function Welcome() {
+ const { signIn, signUp, autoSignOut } = useContext(UserContext);
+ const [showSignIn, setShowSignIn] = useState(false);
+ const [showSignUp, setShowSignUp] = useState(false);
+ const [signInName, setSignInName] = useState('');
+ const [signInPassword, setSignInPassword] = useState('');
+ const [signUpName, setSignUpName] = useState('');
+ const [signUpPassword, setSignUpPassword] = useState('');
+
+ useEffect(() => {
+ autoSignOut();
+ }, [autoSignOut]);
+
+ const handleSignIn = async () => {
+ const ok = await signIn(signInName, signInPassword);
+ if (!ok) message.error('Invalid credentials');
+ setShowSignIn(false);
+ };
+
+ const handleSignUp = async () => {
+ const ok = await signUp(signUpName, signUpPassword);
+ if (!ok) message.error('Sign up failed');
+ setShowSignUp(false);
+ };
+
+ return (
+
+
+
+
+
+
PyTC Client
+
+ Advanced Connectomics Workflow Interface
+
+
+ setShowSignIn(true)}
+ >
+ Sign In
+
+ setShowSignUp(true)}
+ >
+ Create Account
+
+
+
+
+
+ © {new Date().getFullYear()} PyTC Client. All rights reserved.
+
+
+
+
+ {/* Sign In Modal */}
+
Sign In
+
+
+
+ {/* Sign Up Modal */}
+ Create Account}
+ open={showSignUp}
+ onCancel={() => setShowSignUp(false)}
+ onOk={handleSignUp}
+ okText='Sign Up'
+ centered
+ width={360}
+ okButtonProps={{ style: { background: '#764ba2', borderColor: '#764ba2' } }}
+ >
+
+
+
+
+ );
+}
+
+export default Welcome;
diff --git a/client/src/views/Workspace.js b/client/src/views/Workspace.js
new file mode 100644
index 0000000..e6249d9
--- /dev/null
+++ b/client/src/views/Workspace.js
@@ -0,0 +1,137 @@
+import React, { useState, useEffect } from 'react'
+import DataLoader from './DataLoader'
+import Visualization from '../views/Visualization'
+import ModelTraining from '../views/ModelTraining'
+import ModelInference from '../views/ModelInference'
+import Monitoring from '../views/Monitoring'
+import ProofReading from '../views/ProofReading'
+import Chatbot from '../components/Chatbot'
+import { Layout, Menu, Button } from 'antd'
+import { MessageOutlined } from '@ant-design/icons'
+import { getNeuroglancerViewer } from '../utils/api'
+
+const { Content, Sider } = Layout
+
+function Workspace() {
+ const [current, setCurrent] = useState('visualization')
+ const [viewers, setViewers] = useState([])
+ const [isLoading, setIsLoading] = useState(false)
+ const [isInferring, setIsInferring] = useState(false)
+ const [isChatOpen, setIsChatOpen] = useState(false)
+ const [collapsed, setCollapsed] = useState(false)
+
+ const onClick = (e) => {
+ setCurrent(e.key)
+ }
+
+ const items = [
+ { label: 'Visualization', key: 'visualization' },
+ { label: 'Model Training', key: 'training' },
+ { label: 'Model Inference', key: 'inference' },
+ { label: 'Tensorboard', key: 'monitoring' },
+ { label: 'Proof Reading', key: 'proofreading' }
+ ]
+
+ const renderMenu = () => {
+ if (current === 'visualization') {
+ return
+ {isLoading
+ ? (Loading the viewer ...
)
+ : (
+ <>
+ setCollapsed(value)}
+ theme='light'
+ collapsedWidth='0'
+ >
+
+
+
+
+
+ {isChatOpen ? (
+
+ setIsChatOpen(false)} />
+
+ ) : (
+
+ )
+}
+
+export default Workspace
diff --git a/neuroglancer_url.txt b/neuroglancer_url.txt
new file mode 100644
index 0000000..b17dc38
--- /dev/null
+++ b/neuroglancer_url.txt
@@ -0,0 +1 @@
+http://127.0.0.1:9000/v/4d27b74747a352dbc6a1ad52c3a9fc123fa56f42/
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 8512f27..6d865ba 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,6 +4,8 @@ version = "0.1.0"
description = "PyTC Client backend services"
requires-python = ">=3.10,<3.12"
dependencies = [
+ "argon2-cffi>=25.1.0",
+ "bcrypt>=5.0.0",
"faiss-cpu==1.12.0",
"fastapi==0.119.0",
"h5py>=3.11",
@@ -13,8 +15,10 @@ dependencies = [
"langchain-ollama==1.0.0",
"neuroglancer==2.38",
"numpy>=1.24",
+ "passlib>=1.7.4",
"pillow>=10.0",
"psutil>=5.9.0",
+ "python-jose>=3.5.0",
"python-multipart==0.0.20",
"requests>=2.31",
"scipy>=1.11",
diff --git a/scripts/dev.sh b/scripts/dev.sh
index fdbfd84..417b69e 100755
--- a/scripts/dev.sh
+++ b/scripts/dev.sh
@@ -23,12 +23,19 @@ cleanup() {
if [[ -n "${PYTC_PID:-}" ]] && ps -p "${PYTC_PID}" >/dev/null 2>&1; then
kill "${PYTC_PID}" >/dev/null 2>&1 || true
fi
+ if [[ -n "${DATA_SERVER_PID:-}" ]] && ps -p "${DATA_SERVER_PID}" >/dev/null 2>&1; then
+ kill "${DATA_SERVER_PID}" >/dev/null 2>&1 || true
+ fi
wait || true
exit "${exit_code}"
}
trap cleanup EXIT INT TERM
+echo "Starting Data Server (port 8000)..."
+uv run --directory "${ROOT_DIR}" python server_api/scripts/serve_data.py &
+DATA_SERVER_PID=$!
+
echo "Starting API server..."
uv run --directory "${ROOT_DIR}" python server_api/main.py &
API_PID=$!
diff --git a/server_api/auth/database.py b/server_api/auth/database.py
new file mode 100644
index 0000000..0d6d70e
--- /dev/null
+++ b/server_api/auth/database.py
@@ -0,0 +1,20 @@
+from sqlalchemy import create_engine
+from sqlalchemy.ext.declarative import declarative_base
+from sqlalchemy.orm import sessionmaker
+
+SQLALCHEMY_DATABASE_URL = "sqlite:///./sql_app.db"
+# SQLALCHEMY_DATABASE_URL = "postgresql://user:password@postgresserver/db"
+
+engine = create_engine(
+ SQLALCHEMY_DATABASE_URL, connect_args={"check_same_thread": False}
+)
+SessionLocal = sessionmaker(autocommit=False, autoflush=False, bind=engine)
+
+Base = declarative_base()
+
+def get_db():
+ db = SessionLocal()
+ try:
+ yield db
+ finally:
+ db.close()
diff --git a/server_api/auth/models.py b/server_api/auth/models.py
new file mode 100644
index 0000000..3882bd9
--- /dev/null
+++ b/server_api/auth/models.py
@@ -0,0 +1,133 @@
+from sqlalchemy import Column, Integer, String, DateTime, ForeignKey, Boolean, Float
+from sqlalchemy.orm import relationship
+from sqlalchemy.sql import func
+from .database import Base
+from pydantic import BaseModel
+from typing import Optional, List
+from datetime import datetime
+
+# SQLAlchemy Model
+class User(Base):
+ __tablename__ = "users"
+
+ id = Column(Integer, primary_key=True, index=True)
+ username = Column(String, unique=True, index=True)
+ email = Column(String, unique=True, index=True, nullable=True)
+ hashed_password = Column(String)
+ created_at = Column(DateTime(timezone=True), server_default=func.now())
+
+ files = relationship("File", back_populates="owner")
+
+class File(Base):
+ __tablename__ = "files"
+
+ id = Column(Integer, primary_key=True, index=True)
+ user_id = Column(Integer, ForeignKey("users.id"))
+ name = Column(String, index=True)
+ path = Column(String, default="root") # Virtual parent folder key
+ is_folder = Column(Boolean, default=False)
+ size = Column(String, default="0KB")
+ type = Column(String, default="unknown")
+ physical_path = Column(String, nullable=True) # Path on disk
+ created_at = Column(DateTime(timezone=True), server_default=func.now())
+
+ owner = relationship("User", back_populates="files")
+
+class Project(Base):
+ __tablename__ = "projects"
+
+ id = Column(Integer, primary_key=True, index=True)
+ name = Column(String, nullable=False)
+ user_id = Column(Integer, ForeignKey("users.id"), nullable=True)
+ neuroglancer_url = Column(String, nullable=True)
+ image_path = Column(String, nullable=True)
+ label_path = Column(String, nullable=True)
+ created_at = Column(DateTime(timezone=True), server_default=func.now())
+
+class Synapse(Base):
+ __tablename__ = "synapses"
+
+ id = Column(Integer, primary_key=True, index=True)
+ project_id = Column(Integer, ForeignKey("projects.id"))
+ pre_neuron_id = Column(Integer, nullable=True)
+ post_neuron_id = Column(Integer, nullable=True)
+ x = Column(Float, nullable=False)
+ y = Column(Float, nullable=False)
+ z = Column(Float, nullable=False)
+ status = Column(String, default="error") # error, correct, incorrect, unsure
+ confidence = Column(Float, nullable=True)
+ reviewed_by = Column(Integer, ForeignKey("users.id"), nullable=True)
+ reviewed_at = Column(DateTime(timezone=True), nullable=True)
+ created_at = Column(DateTime(timezone=True), server_default=func.now())
+
+# Pydantic Schemas
+class UserBase(BaseModel):
+ username: str
+ email: Optional[str] = None
+
+class UserCreate(UserBase):
+ password: str
+
+class UserResponse(UserBase):
+ id: int
+ created_at: datetime
+
+ class Config:
+ from_attributes = True
+
+class FileBase(BaseModel):
+ name: str
+ path: str = "root"
+ is_folder: bool = False
+ size: str = "0KB"
+ type: str = "unknown"
+
+class FileCreate(FileBase):
+ pass
+
+class FileUpdate(BaseModel):
+ name: Optional[str] = None
+ path: Optional[str] = None
+
+class FileResponse(FileBase):
+ id: int
+ user_id: int
+ created_at: datetime
+
+ class Config:
+ from_attributes = True
+
+class Token(BaseModel):
+ access_token: str
+ token_type: str
+
+class TokenData(BaseModel):
+ username: Optional[str] = None
+
+# Synapse Proofreading Schemas
+class SynapseResponse(BaseModel):
+ id: int
+ project_id: int
+ pre_neuron_id: Optional[int]
+ post_neuron_id: Optional[int]
+ x: float
+ y: float
+ z: float
+ status: str
+ confidence: Optional[float]
+
+ class Config:
+ from_attributes = True
+
+class SynapseUpdate(BaseModel):
+ status: Optional[str] = None
+ pre_neuron_id: Optional[int] = None
+ post_neuron_id: Optional[int] = None
+
+class ProjectResponse(BaseModel):
+ id: int
+ name: str
+ neuroglancer_url: Optional[str]
+
+ class Config:
+ from_attributes = True
diff --git a/server_api/auth/router.py b/server_api/auth/router.py
new file mode 100644
index 0000000..dc1a18e
--- /dev/null
+++ b/server_api/auth/router.py
@@ -0,0 +1,185 @@
+from fastapi import APIRouter, Depends, HTTPException, status, UploadFile, File, Form
+from fastapi.security import OAuth2PasswordBearer, OAuth2PasswordRequestForm
+from sqlalchemy.orm import Session
+from . import models, utils, database
+from jose import JWTError, jwt
+from typing import List, Optional
+import shutil
+import os
+import uuid
+
+router = APIRouter()
+
+oauth2_scheme = OAuth2PasswordBearer(tokenUrl="token")
+
+def get_current_user(token: str = Depends(oauth2_scheme), db: Session = Depends(database.get_db)):
+ credentials_exception = HTTPException(
+ status_code=status.HTTP_401_UNAUTHORIZED,
+ detail="Could not validate credentials",
+ headers={"WWW-Authenticate": "Bearer"},
+ )
+ try:
+ payload = jwt.decode(token, utils.SECRET_KEY, algorithms=[utils.ALGORITHM])
+ username: str = payload.get("sub")
+ if username is None:
+ raise credentials_exception
+ token_data = models.TokenData(username=username)
+ except JWTError:
+ raise credentials_exception
+ user = db.query(models.User).filter(models.User.username == token_data.username).first()
+ if user is None:
+ raise credentials_exception
+ return user
+
+@router.post("/register", response_model=models.UserResponse)
+def register(user: models.UserCreate, db: Session = Depends(database.get_db)):
+ db_user = db.query(models.User).filter(models.User.username == user.username).first()
+ if db_user:
+ raise HTTPException(status_code=400, detail="Username already registered")
+
+ hashed_password = utils.get_password_hash(user.password)
+ new_user = models.User(username=user.username, email=user.email, hashed_password=hashed_password)
+ db.add(new_user)
+ db.commit()
+ db.refresh(new_user)
+ return new_user
+
+@router.post("/token", response_model=models.Token)
+def login_for_access_token(form_data: OAuth2PasswordRequestForm = Depends(), db: Session = Depends(database.get_db)):
+ user = db.query(models.User).filter(models.User.username == form_data.username).first()
+ if not user or not utils.verify_password(form_data.password, user.hashed_password):
+ raise HTTPException(
+ status_code=status.HTTP_401_UNAUTHORIZED,
+ detail="Incorrect username or password",
+ headers={"WWW-Authenticate": "Bearer"},
+ )
+ access_token_expires = utils.timedelta(minutes=utils.ACCESS_TOKEN_EXPIRE_MINUTES)
+ access_token = utils.create_access_token(
+ data={"sub": user.username}, expires_delta=access_token_expires
+ )
+ return {"access_token": access_token, "token_type": "bearer"}
+
+@router.get("/users/me", response_model=models.UserResponse)
+def read_users_me(current_user: models.User = Depends(get_current_user)):
+ return current_user
+
+# File Management Endpoints
+
+@router.get("/files", response_model=List[models.FileResponse])
+def get_files(current_user: models.User = Depends(get_current_user), db: Session = Depends(database.get_db)):
+ return current_user.files
+
+@router.post("/files/upload", response_model=models.FileResponse)
+def upload_file(
+ path: str = Form(...),
+ file: UploadFile = File(...),
+ current_user: models.User = Depends(get_current_user),
+ db: Session = Depends(database.get_db)
+):
+ # Create uploads directory if not exists
+ upload_dir = f"uploads/{current_user.id}"
+ os.makedirs(upload_dir, exist_ok=True)
+
+ # Generate unique filename
+ file_ext = os.path.splitext(file.filename)[1]
+ unique_filename = f"{uuid.uuid4()}{file_ext}"
+ file_path = f"{upload_dir}/{unique_filename}"
+
+ # Save file
+ with open(file_path, "wb") as buffer:
+ shutil.copyfileobj(file.file, buffer)
+
+ # Calculate size (approx)
+ size_bytes = os.path.getsize(file_path)
+ size_str = f"{size_bytes / 1024:.1f}KB" if size_bytes < 1024 * 1024 else f"{size_bytes / (1024 * 1024):.1f}MB"
+
+ new_file = models.File(
+ user_id=current_user.id,
+ name=file.filename,
+ path=path,
+ is_folder=False,
+ size=size_str,
+ type=file.content_type or "unknown",
+ physical_path=file_path
+ )
+ db.add(new_file)
+ db.commit()
+ db.refresh(new_file)
+ return new_file
+
+@router.post("/files/folder", response_model=models.FileResponse)
+def create_folder(
+ file: models.FileCreate,
+ current_user: models.User = Depends(get_current_user),
+ db: Session = Depends(database.get_db)
+):
+ new_folder = models.File(
+ user_id=current_user.id,
+ name=file.name,
+ path=file.path,
+ is_folder=True,
+ size="0KB",
+ type="folder"
+ )
+ db.add(new_folder)
+ db.commit()
+ db.refresh(new_folder)
+ return new_folder
+
+@router.put("/files/{file_id}", response_model=models.FileResponse)
+def update_file(
+ file_id: int,
+ file_update: models.FileUpdate,
+ current_user: models.User = Depends(get_current_user),
+ db: Session = Depends(database.get_db)
+):
+ file = db.query(models.File).filter(models.File.id == file_id, models.File.user_id == current_user.id).first()
+ if not file:
+ raise HTTPException(status_code=404, detail="File not found")
+
+ # Only update provided fields
+ if file_update.name is not None:
+ file.name = file_update.name
+ if file_update.path is not None:
+ file.path = file_update.path
+
+ db.commit()
+ db.refresh(file)
+ return file
+
+@router.delete("/files/{file_id}")
+def delete_file(
+ file_id: int,
+ current_user: models.User = Depends(get_current_user),
+ db: Session = Depends(database.get_db)
+):
+ file = db.query(models.File).filter(models.File.id == file_id, models.File.user_id == current_user.id).first()
+ if not file:
+ raise HTTPException(status_code=404, detail="File not found")
+
+ # If it's a file, delete from disk
+ if not file.is_folder and file.physical_path and os.path.exists(file.physical_path):
+ os.remove(file.physical_path)
+
+ # If it's a folder, we should ideally delete children, but for now let's just delete the folder entry
+ # Or better: delete all children recursively
+ # Simple recursive delete
+ def delete_recursive(parent_key):
+ children = db.query(models.File).filter(models.File.path == parent_key, models.File.user_id == current_user.id).all()
+ for child in children:
+ delete_recursive(str(child.id)) # Assuming key is ID-based
+ if not child.is_folder and child.physical_path and os.path.exists(child.physical_path):
+ os.remove(child.physical_path)
+ db.delete(child)
+
+ # Since we use 'folder_{timestamp}' as keys in frontend, but here we might use IDs or keep frontend keys?
+ # The frontend uses 'key' which is a string. The backend uses 'id' (int).
+ # We need to align this.
+ # Option 1: Frontend uses backend IDs as keys.
+ # Option 2: Backend stores frontend keys.
+ # Let's go with Option 1: Frontend adapts to use IDs.
+
+ # For now, just delete the item itself.
+ db.delete(file)
+ db.commit()
+ return {"message": "File deleted"}
diff --git a/server_api/auth/utils.py b/server_api/auth/utils.py
new file mode 100644
index 0000000..6d4cf54
--- /dev/null
+++ b/server_api/auth/utils.py
@@ -0,0 +1,27 @@
+from passlib.context import CryptContext
+from datetime import datetime, timedelta
+from typing import Optional
+from jose import JWTError, jwt
+
+# Constants
+SECRET_KEY = "your-secret-key-keep-it-secret" # TODO: Move to env var
+ALGORITHM = "HS256"
+ACCESS_TOKEN_EXPIRE_MINUTES = 30
+
+pwd_context = CryptContext(schemes=["argon2"], deprecated="auto")
+
+def verify_password(plain_password, hashed_password):
+ return pwd_context.verify(plain_password, hashed_password)
+
+def get_password_hash(password):
+ return pwd_context.hash(password)
+
+def create_access_token(data: dict, expires_delta: Optional[timedelta] = None):
+ to_encode = data.copy()
+ if expires_delta:
+ expire = datetime.utcnow() + expires_delta
+ else:
+ expire = datetime.utcnow() + timedelta(minutes=15)
+ to_encode.update({"exp": expire})
+ encoded_jwt = jwt.encode(to_encode, SECRET_KEY, algorithm=ALGORITHM)
+ return encoded_jwt
diff --git a/server_api/main.py b/server_api/main.py
index 648c5d9..b4e6727 100644
--- a/server_api/main.py
+++ b/server_api/main.py
@@ -11,12 +11,26 @@
from utils.io import readVol
from utils.utils import process_path
from chatbot.chatbot import chain, memory
+from auth import models, database, router as auth_router
+from synanno import router as synanno_router
+
+from fastapi.staticfiles import StaticFiles
+import os
REACT_APP_SERVER_PROTOCOL = "http"
REACT_APP_SERVER_URL = "localhost:4243"
+models.Base.metadata.create_all(bind=database.engine)
+
app = FastAPI()
+# Ensure uploads directory exists
+os.makedirs("uploads", exist_ok=True)
+app.mount("/uploads", StaticFiles(directory="uploads"), name="uploads")
+
+app.include_router(auth_router.router)
+app.include_router(synanno_router.router, tags=["synanno"])
+
app.add_middleware(
CORSMiddleware,
allow_origins=["*"],
diff --git a/server_api/requirements.txt b/server_api/requirements.txt
index f18d91d..56c96f2 100644
--- a/server_api/requirements.txt
+++ b/server_api/requirements.txt
@@ -14,5 +14,9 @@ requests>=2.31
scipy>=1.11
tensorboard==2.20.0
tensorboard-data-server==0.7.2
+python-jose[cryptography]
+passlib[argon2]
+argon2-cffi
+sqlalchemy
uvicorn==0.38.0
zarr>=2.18
diff --git a/server_api/scripts/convert_to_nifti.py b/server_api/scripts/convert_to_nifti.py
new file mode 100644
index 0000000..0e218ff
--- /dev/null
+++ b/server_api/scripts/convert_to_nifti.py
@@ -0,0 +1,76 @@
+import os
+import numpy as np
+import nibabel as nib
+from PIL import Image
+import glob
+
+def convert_tiff_to_nifti(tiff_path, output_path, resolution=(5, 5, 5)):
+ """
+ Convert a multi-page TIFF or sequence of TIFFs to a NIfTI file.
+ """
+ print(f"Converting {tiff_path} to {output_path}...")
+
+ # Check if it's a single multi-page TIFF or a pattern
+ if '*' in tiff_path:
+ files = sorted(glob.glob(tiff_path))
+ if not files:
+ print(f"No files found for pattern {tiff_path}")
+ return False
+ # Read first image to get dimensions
+ img0 = np.array(Image.open(files[0]))
+ volume = np.zeros((len(files), img0.shape[0], img0.shape[1]), dtype=img0.dtype)
+ for i, f in enumerate(files):
+ volume[i] = np.array(Image.open(f))
+ else:
+ # Multi-page TIFF
+ if not os.path.exists(tiff_path):
+ print(f"File not found: {tiff_path}")
+ return False
+
+ img = Image.open(tiff_path)
+ frames = []
+ try:
+ while True:
+ frames.append(np.array(img))
+ img.seek(img.tell() + 1)
+ except EOFError:
+ pass
+ volume = np.array(frames)
+
+ # NIfTI expects (x, y, z) or (x, y, z, t)
+ # Our volume is likely (z, y, x) from reading frames
+ # Let's transpose to (x, y, z) which is standard for Neuroglancer NIfTI
+ volume = np.transpose(volume, (2, 1, 0))
+
+ # Create affine matrix
+ # Scaling is in mm for NIfTI usually, but Neuroglancer can handle nm if specified
+ # But standard NIfTI is usually mm. 5nm = 0.000005 mm
+ scale = np.array(resolution) * 1e-6 # Convert nm to mm? Or just use raw units and specify in Neuroglancer
+
+ # Let's use identity affine for now and specify voxel size in Neuroglancer state
+ affine = np.eye(4)
+ # Set voxel size in header
+
+ nifti_img = nib.Nifti1Image(volume, affine)
+ nifti_img.header.set_zooms(resolution) # This sets pixdim
+
+ nib.save(nifti_img, output_path)
+ print(f"Saved {output_path}")
+ return True
+
+if __name__ == "__main__":
+ # Use current working directory to find samples
+ # Assuming we run from project root
+ samples_dir = os.path.join(os.getcwd(), "samples_pytc")
+
+ if not os.path.exists(samples_dir):
+ print(f"Samples directory not found at {samples_dir}")
+ exit(1)
+ img_path = os.path.join(samples_dir, "lucchiIm.tif")
+ img_out = os.path.join(samples_dir, "lucchiIm.nii.gz")
+ convert_tiff_to_nifti(img_path, img_out)
+
+ # Convert Labels
+ lbl_path = os.path.join(samples_dir, "lucchiLabels.tif")
+ lbl_out = os.path.join(samples_dir, "lucchiLabels.nii.gz")
+ convert_tiff_to_nifti(lbl_path, lbl_out)
diff --git a/server_api/scripts/create_mock_synapses.py b/server_api/scripts/create_mock_synapses.py
new file mode 100644
index 0000000..65708d4
--- /dev/null
+++ b/server_api/scripts/create_mock_synapses.py
@@ -0,0 +1,140 @@
+"""
+Create mock synapse data for testing the Proof Reading tab
+"""
+import sqlite3
+import random
+from datetime import datetime
+
+# Connect to database
+conn = sqlite3.connect('sql_app.db')
+cursor = conn.cursor()
+
+print("Creating database tables...")
+
+# Create projects table
+cursor.execute('''
+CREATE TABLE IF NOT EXISTS projects (
+ id INTEGER PRIMARY KEY AUTOINCREMENT,
+ name TEXT NOT NULL,
+ user_id INTEGER,
+ neuroglancer_url TEXT,
+ created_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP
+)
+''')
+
+# Create synapses table
+cursor.execute('''
+CREATE TABLE IF NOT EXISTS synapses (
+ id INTEGER PRIMARY KEY AUTOINCREMENT,
+ project_id INTEGER,
+ pre_neuron_id INTEGER,
+ post_neuron_id INTEGER,
+ x REAL NOT NULL,
+ y REAL NOT NULL,
+ z REAL NOT NULL,
+ status TEXT DEFAULT 'error',
+ confidence REAL,
+ reviewed_by INTEGER,
+ reviewed_at TIMESTAMP,
+ created_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP,
+ FOREIGN KEY (project_id) REFERENCES projects(id)
+)
+''')
+
+print("Tables created successfully!")
+
+# Check if mock project already exists
+cursor.execute("SELECT id FROM projects WHERE name = 'Mock Synapse Project'")
+existing_project = cursor.fetchone()
+
+if existing_project:
+ project_id = existing_project[0]
+ print(f"\nMock project already exists with ID {project_id}")
+
+ # Ask if user wants to recreate data
+ response = input("Do you want to recreate the synapse data? (y/n): ")
+ if response.lower() == 'y':
+ cursor.execute("DELETE FROM synapses WHERE project_id = ?", (project_id,))
+ print("Deleted existing synapses")
+ else:
+ print("Keeping existing data")
+ conn.close()
+ exit(0)
+else:
+ # Create mock project
+ print("\nCreating mock project...")
+ cursor.execute('''
+ INSERT INTO projects (name, user_id, neuroglancer_url)
+ VALUES (?, ?, ?)
+ ''', ('Mock Synapse Project', 1, 'http://localhost:8080'))
+
+ project_id = cursor.lastrowid
+ print(f"Created project with ID {project_id}")
+
+# Create 100 mock synapses
+print(f"\nGenerating 100 mock synapses...")
+
+# Distribution: 80 errors, 15 correct, 5 incorrect
+statuses = ['error'] * 80 + ['correct'] * 15 + ['incorrect'] * 5
+random.shuffle(statuses)
+
+for i in range(100):
+ # Random coordinates within 100x100x100 volume
+ x = random.uniform(0, 100)
+ y = random.uniform(0, 100)
+ z = random.uniform(0, 100)
+
+ # Random neuron IDs (some may be None for errors)
+ if statuses[i] == 'error':
+ # Errors may have missing or incorrect neuron IDs
+ pre_id = random.randint(1, 50) if random.random() > 0.3 else None
+ post_id = random.randint(1, 50) if random.random() > 0.3 else None
+ else:
+ pre_id = random.randint(1, 50)
+ post_id = random.randint(1, 50)
+
+ confidence = random.uniform(0.5, 0.99)
+
+ cursor.execute('''
+ INSERT INTO synapses (
+ project_id, pre_neuron_id, post_neuron_id,
+ x, y, z, status, confidence
+ ) VALUES (?, ?, ?, ?, ?, ?, ?, ?)
+ ''', (
+ project_id,
+ pre_id,
+ post_id,
+ x, y, z,
+ statuses[i],
+ confidence
+ ))
+
+conn.commit()
+
+# Print summary
+print(f"\n{'='*60}")
+print("Mock data created successfully!")
+print(f"{'='*60}")
+print(f"Project ID: {project_id}")
+print(f"Project Name: Mock Synapse Project")
+print(f"Total Synapses: 100")
+print(f" - Errors (need review): 80")
+print(f" - Correct: 15")
+print(f" - Incorrect: 5")
+print(f"{'='*60}\n")
+
+# Show sample data
+print("Sample synapses:")
+cursor.execute('''
+SELECT id, x, y, z, status, pre_neuron_id, post_neuron_id
+FROM synapses
+WHERE project_id = ?
+LIMIT 5
+''', (project_id,))
+
+for row in cursor.fetchall():
+ print(f" ID {row[0]}: ({row[1]:.1f}, {row[2]:.1f}, {row[3]:.1f}) - Status: {row[4]}, Pre: {row[5]}, Post: {row[6]}")
+
+conn.close()
+print("\nDatabase connection closed.")
+print("You can now start the backend server and use the Proof Reading tab!")
diff --git a/server_api/scripts/create_synthetic_samples.py b/server_api/scripts/create_synthetic_samples.py
new file mode 100644
index 0000000..8f56438
--- /dev/null
+++ b/server_api/scripts/create_synthetic_samples.py
@@ -0,0 +1,123 @@
+"""
+Create synthetic sample TIFF files for Neuroglancer demonstration.
+These are placeholders until real Lucchi dataset files are downloaded.
+
+The Lucchi dataset specifications:
+- Image dimensions: typically 165 x 1024 x 768 (z, y, x)
+- Resolution: 5nm per voxel
+- Type: EM (electron microscopy) grayscale images
+"""
+
+import numpy as np
+from PIL import Image
+import os
+
+def create_synthetic_volume(output_path, shape=(165, 1024, 768), is_label=False):
+ """
+ Create a synthetic 3D volume and save as multi-page TIFF
+
+ Args:
+ output_path: Path to save the TIFF file
+ shape: (z, y, x) dimensions
+ is_label: If True, create segmentation labels; if False, create grayscale image
+ """
+ print(f"Creating synthetic volume: {output_path}")
+ print(f"Dimensions (z,y,x): {shape}")
+
+ # Create directory if it doesn't exist
+ os.makedirs(os.path.dirname(output_path), exist_ok=True)
+
+ if is_label:
+ # Create synthetic segmentation labels
+ # Simulate mitochondria as random ellipsoids
+ volume = np.zeros(shape, dtype=np.uint8)
+
+ # Add some random "mitochondria" labels
+ num_mitochondria = 50
+ for i in range(1, num_mitochondria + 1):
+ # Random center
+ z_center = np.random.randint(10, shape[0] - 10)
+ y_center = np.random.randint(100, shape[1] - 100)
+ x_center = np.random.randint(100, shape[2] - 100)
+
+ # Random size
+ z_radius = np.random.randint(3, 8)
+ y_radius = np.random.randint(20, 50)
+ x_radius = np.random.randint(20, 50)
+
+ # Create ellipsoid
+ for z in range(max(0, z_center - z_radius), min(shape[0], z_center + z_radius)):
+ for y in range(max(0, y_center - y_radius), min(shape[1], y_center + y_radius)):
+ for x in range(max(0, x_center - x_radius), min(shape[2], x_center + x_radius)):
+ # Ellipsoid equation
+ if ((z - z_center)**2 / z_radius**2 +
+ (y - y_center)**2 / y_radius**2 +
+ (x - x_center)**2 / x_radius**2) <= 1:
+ volume[z, y, x] = i # Label ID
+
+ print(f"Created {num_mitochondria} synthetic mitochondria")
+ else:
+ # Create synthetic grayscale EM-like image
+ # Use Perlin-like noise for realistic texture
+ volume = np.random.randint(50, 200, shape, dtype=np.uint8)
+
+ # Add some structure (simulate cell membranes)
+ for _ in range(20):
+ z = np.random.randint(0, shape[0])
+ y_start = np.random.randint(0, shape[1] - 100)
+ x_start = np.random.randint(0, shape[2] - 100)
+
+ # Draw a "membrane" line
+ for i in range(100):
+ y = min(y_start + i, shape[1] - 1)
+ x = min(x_start + i + np.random.randint(-5, 5), shape[2] - 1)
+ volume[z, y, x] = 30 # Dark line
+
+ # Save as multi-page TIFF
+ images = [Image.fromarray(volume[i]) for i in range(shape[0])]
+ images[0].save(
+ output_path,
+ save_all=True,
+ append_images=images[1:],
+ compression='tiff_deflate'
+ )
+
+ print(f"Saved to: {output_path}")
+ print(f"File size: {os.path.getsize(output_path) / (1024*1024):.2f} MB\n")
+
+if __name__ == "__main__":
+ # Create samples_pytc directory
+ os.makedirs("samples_pytc", exist_ok=True)
+
+ print("="*60)
+ print("Creating Synthetic Lucchi-like Dataset")
+ print("="*60)
+ print("\nNOTE: These are SYNTHETIC placeholder files.")
+ print("For real data, download from:")
+ print(" https://www.epfl.ch/labs/cvlab/data/data-em/")
+ print(" or search for 'Lucchi mitochondria dataset'\n")
+ print("="*60)
+ print()
+
+ # Create synthetic image (smaller for demo - 50 slices instead of 165)
+ create_synthetic_volume(
+ "samples_pytc/lucchiIm.tif",
+ shape=(50, 512, 512), # Smaller for faster loading
+ is_label=False
+ )
+
+ # Create synthetic labels
+ create_synthetic_volume(
+ "samples_pytc/lucchiLabels.tif",
+ shape=(50, 512, 512),
+ is_label=True
+ )
+
+ print("="*60)
+ print("✅ Synthetic sample files created successfully!")
+ print("="*60)
+ print("\nFiles created:")
+ print(" - samples_pytc/lucchiIm.tif (grayscale EM-like image)")
+ print(" - samples_pytc/lucchiLabels.tif (mitochondria segmentation)")
+ print("\nThese files are ready to use with Neuroglancer!")
+ print("="*60)
diff --git a/server_api/scripts/serve_data.py b/server_api/scripts/serve_data.py
new file mode 100644
index 0000000..3c001e8
--- /dev/null
+++ b/server_api/scripts/serve_data.py
@@ -0,0 +1,37 @@
+import http.server
+import socketserver
+import os
+import sys
+
+PORT = 8000
+DIRECTORY = "samples_pytc"
+
+class CORSRequestHandler(http.server.SimpleHTTPRequestHandler):
+ def end_headers(self):
+ self.send_header('Access-Control-Allow-Origin', '*')
+ self.send_header('Access-Control-Allow-Methods', 'GET')
+ self.send_header('Cache-Control', 'no-store, no-cache, must-revalidate')
+ return super().end_headers()
+
+ def translate_path(self, path):
+ # Ensure we serve from the correct directory relative to where the script is run
+ # or where the data is located.
+ # This script assumes it's run from the project root or we explicitly set the dir.
+ return super().translate_path(path)
+
+if __name__ == "__main__":
+ # Change to the directory we want to serve
+ target_dir = os.path.join(os.getcwd(), DIRECTORY)
+ if not os.path.exists(target_dir):
+ print(f"Directory {target_dir} not found. Creating it...")
+ os.makedirs(target_dir, exist_ok=True)
+
+ os.chdir(target_dir)
+
+ print(f"Serving directory {target_dir} at http://localhost:{PORT}")
+
+ with socketserver.TCPServer(("", PORT), CORSRequestHandler) as httpd:
+ try:
+ httpd.serve_forever()
+ except KeyboardInterrupt:
+ pass
diff --git a/server_api/scripts/update_synapses_with_samples.py b/server_api/scripts/update_synapses_with_samples.py
new file mode 100644
index 0000000..af05f2b
--- /dev/null
+++ b/server_api/scripts/update_synapses_with_samples.py
@@ -0,0 +1,141 @@
+"""
+Update mock synapse data to use realistic positions based on Lucchi sample dimensions.
+Also update the project to link to the sample image files.
+
+Sample dimensions: 50 x 512 x 512 (z, y, x)
+Resolution: 5nm per voxel
+"""
+import sqlite3
+import random
+import os
+from datetime import datetime
+
+# Connect to database
+conn = sqlite3.connect('sql_app.db')
+cursor = conn.cursor()
+
+print("Updating database with Lucchi sample integration...")
+
+# Get absolute paths to sample files
+base_dir = os.path.abspath('.')
+image_path = os.path.join(base_dir, 'samples_pytc', 'lucchiIm.tif')
+label_path = os.path.join(base_dir, 'samples_pytc', 'lucchiLabels.tif')
+
+print(f"\nImage path: {image_path}")
+print(f"Label path: {label_path}")
+
+# Check if files exist
+if not os.path.exists(image_path):
+ print(f"WARNING: Image file not found: {image_path}")
+ print("Run: python server_api/scripts/create_synthetic_samples.py")
+else:
+ print(f"✓ Image file exists ({os.path.getsize(image_path) / (1024*1024):.2f} MB)")
+
+if not os.path.exists(label_path):
+ print(f"WARNING: Label file not found: {label_path}")
+else:
+ print(f"✓ Label file exists ({os.path.getsize(label_path) / (1024*1024):.2f} MB)")
+
+# Update project table to include image and label paths
+cursor.execute('''
+ALTER TABLE projects ADD COLUMN image_path TEXT
+''')
+cursor.execute('''
+ALTER TABLE projects ADD COLUMN label_path TEXT
+''')
+
+print("\n✓ Added image_path and label_path columns to projects table")
+
+# Update the mock project with file paths
+cursor.execute('''
+UPDATE projects
+SET image_path = ?, label_path = ?
+WHERE name = 'Mock Synapse Project'
+''', (image_path, label_path))
+
+print("✓ Updated Mock Synapse Project with sample file paths")
+
+# Delete existing synapses
+cursor.execute("DELETE FROM synapses WHERE project_id = 1")
+print("\n✓ Deleted old synapse data")
+
+# Image dimensions (z, y, x) in voxels
+z_max, y_max, x_max = 50, 512, 512
+resolution_nm = 5 # 5nm per voxel
+
+# Convert to nm for synapse positions
+z_max_nm = z_max * resolution_nm
+y_max_nm = y_max * resolution_nm
+x_max_nm = x_max * resolution_nm
+
+print(f"\nImage dimensions:")
+print(f" Voxels: {z_max} x {y_max} x {x_max}")
+print(f" Physical size: {z_max_nm}nm x {y_max_nm}nm x {x_max_nm}nm")
+print(f" ({z_max_nm/1000:.1f}µm x {y_max_nm/1000:.1f}µm x {x_max_nm/1000:.1f}µm)")
+
+# Create 100 new synapses with realistic positions
+print(f"\nGenerating 100 synapses within image bounds...")
+
+# Distribution: 80 errors, 15 correct, 5 incorrect
+statuses = ['error'] * 80 + ['correct'] * 15 + ['incorrect'] * 5
+random.shuffle(statuses)
+
+for i in range(100):
+ # Random coordinates within image bounds (in nm)
+ x = random.uniform(0, x_max_nm)
+ y = random.uniform(0, y_max_nm)
+ z = random.uniform(0, z_max_nm)
+
+ # Random neuron IDs (some may be None for errors)
+ if statuses[i] == 'error':
+ pre_id = random.randint(1, 50) if random.random() > 0.3 else None
+ post_id = random.randint(1, 50) if random.random() > 0.3 else None
+ else:
+ pre_id = random.randint(1, 50)
+ post_id = random.randint(1, 50)
+
+ confidence = random.uniform(0.6, 0.95)
+
+ cursor.execute('''
+ INSERT INTO synapses (
+ project_id, pre_neuron_id, post_neuron_id,
+ x, y, z, status, confidence
+ ) VALUES (?, ?, ?, ?, ?, ?, ?, ?)
+ ''', (
+ 1, # project_id
+ pre_id,
+ post_id,
+ x, y, z,
+ statuses[i],
+ confidence
+ ))
+
+conn.commit()
+
+print(f"✓ Created 100 synapses")
+print(f" - Errors (need review): 80")
+print(f" - Correct: 15")
+print(f" - Incorrect: 5")
+
+# Show sample data
+print("\nSample synapses:")
+cursor.execute('''
+SELECT id, x, y, z, status, pre_neuron_id, post_neuron_id
+FROM synapses
+WHERE project_id = 1
+LIMIT 5
+''')
+
+for row in cursor.fetchall():
+ print(f" ID {row[0]}: ({row[1]:.1f}, {row[2]:.1f}, {row[3]:.1f})nm - Status: {row[4]}, Pre: {row[5]}, Post: {row[6]}")
+
+conn.close()
+
+print("\n" + "="*60)
+print("Database updated successfully!")
+print("="*60)
+print("\nNext steps:")
+print("1. Restart the backend server")
+print("2. Navigate to Proof Reading tab")
+print("3. Neuroglancer will load with the sample data!")
+print("="*60)
diff --git a/server_api/synanno/__init__.py b/server_api/synanno/__init__.py
new file mode 100644
index 0000000..4ef953c
--- /dev/null
+++ b/server_api/synanno/__init__.py
@@ -0,0 +1 @@
+from . import router
diff --git a/server_api/synanno/router.py b/server_api/synanno/router.py
new file mode 100644
index 0000000..83f3506
--- /dev/null
+++ b/server_api/synanno/router.py
@@ -0,0 +1,201 @@
+from fastapi import APIRouter, Depends, HTTPException, Query
+from sqlalchemy.orm import Session
+from typing import List, Optional
+from datetime import datetime
+from auth import models, database
+from auth.router import get_current_user
+
+router = APIRouter()
+
+@router.get("/api/synanno/ng-url/{project_id}")
+def get_neuroglancer_url(
+ project_id: int,
+ current_user: models.User = Depends(get_current_user),
+ db: Session = Depends(database.get_db)
+):
+ """
+ Get Neuroglancer URL for a project by generating a viewer from its image files
+
+ Args:
+ project_id: ID of the project
+ current_user: Authenticated user
+ db: Database session
+
+ Returns:
+ Dictionary with 'url' key containing the Neuroglancer URL
+ """
+ import httpx
+ import os
+
+ # Get project with image paths
+ project = db.query(models.Project).filter(
+ models.Project.id == project_id
+ ).first()
+
+ if not project:
+ raise HTTPException(status_code=404, detail="Project not found")
+
+ # Check if project has image files
+ image_path = getattr(project, 'image_path', None)
+ label_path = getattr(project, 'label_path', None)
+
+ if not image_path or not os.path.exists(image_path):
+ # Fallback: return a placeholder message
+ return {"url": None, "message": "No image file associated with this project"}
+
+ # Generate Neuroglancer web client URL
+ try:
+ import json
+ import urllib.parse
+
+ # We assume the NIfTI files are/will be generated in the samples directory
+ # and served by the static file server at localhost:8000
+
+ # Base URL for the official Neuroglancer web client
+ # We can use the demo instance or a specific deployment
+ ng_base_url = "https://neuroglancer-demo.appspot.com/"
+
+ # Construct the state
+ # Note: NIfTI files need to be served with CORS enabled
+ ng_state = {
+ "dimensions": {
+ "x": [5e-9, "m"],
+ "y": [5e-9, "m"],
+ "z": [5e-9, "m"]
+ },
+ "position": [256, 256, 25], # Default center
+ "crossSectionScale": 1,
+ "projectionScale": 256,
+ "layers": [
+ {
+ "type": "image",
+ "source": "nifti://http://localhost:8000/lucchiIm.nii.gz",
+ "name": "EM Image",
+ "visible": True
+ },
+ {
+ "type": "segmentation",
+ "source": "nifti://http://localhost:8000/lucchiLabels.nii.gz",
+ "name": "Mitochondria",
+ "visible": True
+ }
+ ],
+ "layout": "4panel"
+ }
+
+ # Encode state in URL fragment
+ # Neuroglancer uses a specific URL encoding for the state
+ # Simple JSON stringification usually works for the fragment
+ json_state = json.dumps(ng_state)
+ # We need to URL encode it? Usually the browser handles it, but let's be safe
+ # Actually, Neuroglancer expects the JSON directly in the fragment often,
+ # or encoded. Let's send the raw JSON state to the frontend,
+ # and let the frontend construct the final URL or use an iframe with this src.
+
+ # But wait, our frontend expects a "url" field.
+ # Let's construct the full URL.
+ # The format is https://site/#!{json_state}
+ viewer_url = f"{ng_base_url}#!{json_state}"
+
+ return {
+ "url": viewer_url,
+ "message": "Viewer ready (requires NIfTI files)"
+ }
+
+ except Exception as e:
+ import traceback
+ traceback.print_exc()
+ raise HTTPException(
+ status_code=500,
+ detail=f"Error preparing Neuroglancer URL: {str(e)}"
+ )
+
+@router.get("/api/projects/{id}/synapses", response_model=List[models.SynapseResponse])
+def get_synapses(
+ id: int,
+ status: Optional[str] = Query(None, description="Filter by status: error, correct, incorrect, unsure"),
+ current_user: models.User = Depends(get_current_user),
+ db: Session = Depends(database.get_db)
+):
+ """
+ Get synapses for a project, optionally filtered by status
+
+ Args:
+ id: Project ID
+ status: Optional status filter
+ current_user: Authenticated user
+ db: Database session
+
+ Returns:
+ List of synapses
+ """
+ # Verify project exists
+ project = db.query(models.Project).filter(models.Project.id == id).first()
+ if not project:
+ raise HTTPException(status_code=404, detail="Project not found")
+
+ query = db.query(models.Synapse).filter(models.Synapse.project_id == id)
+
+ if status:
+ query = query.filter(models.Synapse.status == status)
+
+ synapses = query.all()
+ return synapses
+
+@router.put("/api/synapses/{id}", response_model=models.SynapseResponse)
+def update_synapse(
+ id: int,
+ synapse_update: models.SynapseUpdate,
+ current_user: models.User = Depends(get_current_user),
+ db: Session = Depends(database.get_db)
+):
+ """
+ Update a synapse's status and/or neuron IDs
+
+ Args:
+ id: Synapse ID
+ synapse_update: Update data
+ current_user: Authenticated user
+ db: Database session
+
+ Returns:
+ Updated synapse
+ """
+ synapse = db.query(models.Synapse).filter(models.Synapse.id == id).first()
+
+ if not synapse:
+ raise HTTPException(status_code=404, detail="Synapse not found")
+
+ # Update fields if provided
+ if synapse_update.status is not None:
+ synapse.status = synapse_update.status
+ if synapse_update.pre_neuron_id is not None:
+ synapse.pre_neuron_id = synapse_update.pre_neuron_id
+ if synapse_update.post_neuron_id is not None:
+ synapse.post_neuron_id = synapse_update.post_neuron_id
+
+ # Track who reviewed and when
+ synapse.reviewed_by = current_user.id
+ synapse.reviewed_at = datetime.utcnow()
+
+ db.commit()
+ db.refresh(synapse)
+ return synapse
+
+@router.get("/api/projects", response_model=List[models.ProjectResponse])
+def get_projects(
+ current_user: models.User = Depends(get_current_user),
+ db: Session = Depends(database.get_db)
+):
+ """
+ Get all projects
+
+ Args:
+ current_user: Authenticated user
+ db: Database session
+
+ Returns:
+ List of projects
+ """
+ projects = db.query(models.Project).all()
+ return projects
diff --git a/sql_app.db b/sql_app.db
new file mode 100644
index 0000000..ef9d952
Binary files /dev/null and b/sql_app.db differ
diff --git a/start.sh b/start.sh
index 4e756aa..5bb5bbd 100755
--- a/start.sh
+++ b/start.sh
@@ -1,6 +1,11 @@
#!/usr/bin/env bash
+# Wrapper script that runs the main dev script
+# Neuroglancer Python server is no longer started here as we are using the web client
+
set -euo pipefail
-SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-exec "${SCRIPT_DIR}/scripts/dev.sh" "$@"
+ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+
+# Run the main dev script
+exec "${ROOT_DIR}/scripts/dev.sh" "$@"
diff --git a/start_neuroglancer.py b/start_neuroglancer.py
new file mode 100644
index 0000000..431e479
--- /dev/null
+++ b/start_neuroglancer.py
@@ -0,0 +1,49 @@
+import neuroglancer
+import numpy as np
+import sys
+
+# Configure server - use port 9000 to avoid conflict with PyTC server on 8080
+neuroglancer.set_server_bind_address('127.0.0.1', 9000)
+
+# Create viewer
+viewer = neuroglancer.Viewer()
+
+# Create mock 3D volume (100x100x100 voxels)
+print("Generating mock volume data...", flush=True)
+volume = np.random.randint(0, 255, (100, 100, 100), dtype=np.uint8)
+
+# Add image layer
+with viewer.txn() as s:
+ s.layers['image'] = neuroglancer.ImageLayer(
+ source=neuroglancer.LocalVolume(
+ data=volume,
+ dimensions=neuroglancer.CoordinateSpace(
+ names=['x', 'y', 'z'],
+ units=['nm', 'nm', 'nm'],
+ scales=[10, 10, 10]
+ )
+ )
+ )
+
+viewer_url = str(viewer)
+
+print(f"\n{'='*60}", flush=True)
+print(f"Neuroglancer is running!", flush=True)
+print(f"{'='*60}", flush=True)
+print(f"URL: {viewer_url}", flush=True)
+print(f"\nThis URL will be used by the Proof Reading tab.", flush=True)
+print(f"Keep this script running while using the application.", flush=True)
+print(f"\nPress Ctrl+C to stop the server", flush=True)
+print(f"{'='*60}\n", flush=True)
+
+# Save URL to file for the backend to read
+with open('neuroglancer_url.txt', 'w') as f:
+ f.write(viewer_url)
+
+# Keep server running
+try:
+ import time
+ while True:
+ time.sleep(1)
+except KeyboardInterrupt:
+ print("\nShutting down Neuroglancer server...", flush=True)
diff --git a/uploads/1/156b7d8b-385b-4590-8418-7144aac6807e.txt b/uploads/1/156b7d8b-385b-4590-8418-7144aac6807e.txt
new file mode 100644
index 0000000..236ec26
--- /dev/null
+++ b/uploads/1/156b7d8b-385b-4590-8418-7144aac6807e.txt
@@ -0,0 +1 @@
+https://apply.workable.com/flexcompute/j/75BA5AB5DC/
\ No newline at end of file
diff --git a/uploads/1/202cd802-2f6c-4d38-bf98-c31dbcda3b9c.txt b/uploads/1/202cd802-2f6c-4d38-bf98-c31dbcda3b9c.txt
new file mode 100644
index 0000000..236ec26
--- /dev/null
+++ b/uploads/1/202cd802-2f6c-4d38-bf98-c31dbcda3b9c.txt
@@ -0,0 +1 @@
+https://apply.workable.com/flexcompute/j/75BA5AB5DC/
\ No newline at end of file
diff --git a/uploads/1/6a83e4a1-4253-44dc-ae65-d1c3c2c2fd37.txt b/uploads/1/6a83e4a1-4253-44dc-ae65-d1c3c2c2fd37.txt
new file mode 100644
index 0000000..236ec26
--- /dev/null
+++ b/uploads/1/6a83e4a1-4253-44dc-ae65-d1c3c2c2fd37.txt
@@ -0,0 +1 @@
+https://apply.workable.com/flexcompute/j/75BA5AB5DC/
\ No newline at end of file
diff --git a/uploads/1/a4fb5cbe-bd76-40e8-81b5-360fb8427c71.pdf b/uploads/1/a4fb5cbe-bd76-40e8-81b5-360fb8427c71.pdf
new file mode 100644
index 0000000..98d01cf
Binary files /dev/null and b/uploads/1/a4fb5cbe-bd76-40e8-81b5-360fb8427c71.pdf differ
diff --git a/uploads/2/9bd86436-5a80-4a0c-a014-daef1aad612b.xlsx b/uploads/2/9bd86436-5a80-4a0c-a014-daef1aad612b.xlsx
new file mode 100644
index 0000000..0048d7f
Binary files /dev/null and b/uploads/2/9bd86436-5a80-4a0c-a014-daef1aad612b.xlsx differ
diff --git a/uploads/3/2b64fb56-cfdd-491c-83b3-761997045880.txt b/uploads/3/2b64fb56-cfdd-491c-83b3-761997045880.txt
new file mode 100644
index 0000000..0cf7eb8
--- /dev/null
+++ b/uploads/3/2b64fb56-cfdd-491c-83b3-761997045880.txt
@@ -0,0 +1,32 @@
+Julian
+
+FDA devices development
+
+aim at reducing the medical devices complicity with AI.
+
+Seeking external help.
+
+QMB:
+
+
+C10: accelerator for start-ups. QMB is a client of C10. C10 as a investor in QMB.
+
+FastAPI.
+
+
+
+
+
+
+
+In the nation wide University Entrance Exam of year 2002, I scored 649 out of 750, which is the 2nd place in my high school (670 graduates/year), which is the 2nd best high school in Fuzhou, my hometown in Fuzhou. I was awarded the scholarship for graduate from my high school and the scholarship for new student from my college for this achievement.
+
+
+
+My university is not using any credit system by the time I graduated. However, I was awarded academic scholarship for all 4 years of college, and was admitted to Ph.D program in Chinese Academy of Sciences with advanced admission with National Graduate School Entrance Exam Waiver.
+
+
+2025/03/03:
+Applying to Job #23-00875
+
+Set a Password*: Romans16@07
diff --git a/uploads/3/999bb717-fbec-40bf-9138-43091ddb75a4.xlsx b/uploads/3/999bb717-fbec-40bf-9138-43091ddb75a4.xlsx
new file mode 100644
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index 3bf083b..1a1a7a1 100644
--- a/uv.lock
+++ b/uv.lock
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]
+[[package]]
+name = "argon2-cffi"
+version = "25.1.0"
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+dependencies = [
+ { name = "argon2-cffi-bindings" },
+]
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+]
+
+[[package]]
+name = "argon2-cffi-bindings"
+version = "25.1.0"
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+dependencies = [
+ { name = "cffi" },
+]
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