Cherry Studio Setup Guide

1. In Cherry Studio, click the Settings icon (gear icon)
2. In the settings menu, select API Keys

1. In the API Keys panel, click the Add Provider button
2. Select your provider, such as Google AI Studio or OpenRouter.

1. A configuration window will appear
2. Paste your API key into the field (starts with sk- or similar)
3. Click the Test Connection button - you should see a green "Success" message
4. Click Save

You're now ready to use AI models in Cherry Studio.

Optional: if you want direct access to DeepSeek models:

1. Click Add Provider → DeepSeek
2. Create account at platform.deepseek.com
3. Recommended Model: deepseek-v4-flash if it is available; otherwise choose the DeepSeek model your provider marks as the default or recommended option.
4. Note: You can also access all DeepSeek models via OpenRouter.

Optional: for direct access to Kimi models:

1. Click Add Provider → Custom
2. Name: "Moonshot AI (Kimi)"
3. Create account at platform.moonshot.ai
4. Base URL: https://api.moonshot.ai/v1
5. Recommended Model: kimi-k2.7-code for coding tasks, or kimi-k2.6 for general multimodal work
6. Note: You can also access Kimi models via OpenRouter.

Recommended free backup for generous daily limits:

1. Create account at aistudio.google.com
2. Get API key at aistudio.google.com/app/apikey
3. In Cherry Studio: Add Provider → Google Gemini
4. Paste your API key (starts with AIza…)

Available models:

• gemini-3.5-flash (stable default for strong general work)
• gemini-3.1-pro-preview (preview for complex analysis)
• gemini-3-flash-preview (preview for lower-cost frontier-class work)
• Gemini embedding models (document similarity)

Use cases:

• Processing large literature collections (1M token context)
• Backup when course API credits are low
• Cost-free experimentation
• Document embeddings and semantic search

Daily limits reset at midnight Pacific Time.

1. Ensure you're running Cherry Studio v1.5.7 or higher
2. Settings → Navigation → Set navigation bar to Top position
3. Create a new tab or conversation
4. Click the Code (</>) icon in the toolbar

Choose from available CLI tools:

• Claude Code: Premium, excellent for research workflows
• Antigravity CLI: Google's terminal-agent tool, the successor to the former consumer Gemini CLI
• Qwen Code: Alibaba's open-source alternative
• OpenAI Codex: GPT-based coding agent

For Research Memex, we recommend:

• Beginners → Cherry Studio first, then Antigravity CLI if you want Google's terminal agent
• Advanced → Claude Code
• Experimenters → Qwen Code (open source)

1. Select a compatible AI model from your configured providers
2. Set working directory (your research project folder)
3. Configure environment variables if needed
4. Click Launch Agent
5. The CLI agent runs in an embedded terminal within Cherry Studio.

1. Click New Chat in the sidebar

2. Select a model (start with Gemini 3.5 Flash, Claude Sonnet 5, or your provider's current default DeepSeek model)

3. Type this test prompt:

   Please summarize the key components of a systematic review
   according to PRISMA guidelines in 3 bullet points.

   Copy

4. Press Enter or click Send

Expected response: you should receive a concise summary within 5-10 seconds.

Test each configured model:

1. Create new conversation
2. Select different model from dropdown
3. Send same test prompt
4. Compare responses

Verify MCP servers are working:

1. Test Zotero: "Search my Zotero for systematic review papers"
2. Test Sequential Thinking: "Help me plan a literature review in 5 steps using sequential thinking"
3. Test Web Search: "Find recent papers on AI in management"

Expected: each command should return relevant results.

1. Export your curated papers from Zotero as PDFs
2. Create a folder: systematic-review-papers
3. Place all PDFs in this folder

1. Click Knowledge Base in sidebar
2. Click Create New Collection
3. Name it: "My Systematic Review"
4. Click Add Documents
5. Select your PDF folder
6. Wait for processing (1-2 min per 10 papers)

Advanced options:

• OCR processing: enable for scanned PDFs (requires v1.4.8+)
• intent recognition: improves search accuracy with stronger models
• multiple formats: supports PDF, TXT, Markdown, Word, and other formats

See: Knowledge Base Documentation | Document Preprocessing

1. Start new conversation
2. Click the Knowledge icon in the chat toolbar
3. Select your collection
4. The AI now has access to your papers.

Tip: enable "Intent Recognition" in knowledge base settings for more accurate search results when asking complex research questions.

Obsidian is a markdown editor for connected research notes:

• local storage: your notes stay on your computer
• bidirectional linking: connect ideas across papers
• Zotero integration: citation management
• graph view: visualize connections in your research
• MCP accessibility: AI can read your knowledge base

For detailed instructions, see the Obsidian Setup Guide.

Essential steps:

1. Install Obsidian from obsidian.md
2. Create vault: "Systematic-Review-Research"
3. Install plugins:
   • Zotero Integration (multiple options available)
   • Dataview (for literature tables)
   • Local REST API (for MCP access)
4. Configure integration with Zotero (requires Better BibTeX)
5. Set up MCP for Cherry Studio access

Set Up Folder Structure

Create this structure in your Obsidian vault:

/Research/
  /01-Literature-Notes/      # Individual paper notes from Zotero
  /02-AI-Conversations/       # Exported Cherry Studio chats
  /03-Synthesis/             # Your analysis and connections
  /04-Protocol/              # Review protocol development
  /05-Daily-Notes/           # Research journal
  /Templates/                # Note templates

Export from Cherry Studio to Obsidian

1. In Cherry Studio conversation:

   • Click Export button (or Cmd/Ctrl + E)
   • Choose Markdown format
   • Select Save to Folder
   • Navigate to /02-AI-Conversations/
   • Name format: YYYY-MM-DD-Topic.md

2. The exported file includes:

   • Complete conversation history
   • Model used and timestamps
   • Any code blocks or tables
   • Referenced papers (if using Zotero MCP)

Create Literature Note Template

Save this in /Templates/literature-note.md:

# {{title}}

## Metadata
- **Authors**: {{authors}}
- **Year**: {{year}}
- **Journal**: {{publicationTitle}}
- **DOI**: {{DOI}}
- **Tags**: {{tags}}
- **Zotero**: [Open in Zotero]({{zoteroLink}})

## Summary
*AI-generated or your summary*

## Key Contributions
-

## Methodology
-

## Limitations
-

## Relevance to My Research
-

## Connections
- Related papers:
- Contradicts:
- Extends:

## Annotations
{{annotations}}

• From Zotero to Obsidian: Import papers with annotations
• From Cherry Studio to Obsidian: Export AI analysis
• Within Obsidian: Link papers, find patterns, build arguments
• Back to Cherry Studio: Copy synthesis for further AI analysis

Advanced integration: Cherry Studio can also connect directly to Obsidian via MCP or data settings. See: Cherry Studio Obsidian Integration

• Double-check you copied the key completely, with no extra spaces
• Ensure you have credits in your account
• Try regenerating the API key

• Wait 60 seconds and try again
• Switch to a different model temporarily
• Check your API provider's rate limits

• Check internet connection
• Verify firewall isn't blocking Cherry Studio
• Try using a different API provider

• Ensure PDFs are text-based (not scanned images)
• Check file size (max 10MB per file recommended)
• Try re-importing documents

• Check API key configuration
• Verify you have credits remaining
• Try a different model to isolate issue

• New Chat: Cmd/Ctrl + N
• Fork Conversation: Cmd/Ctrl + Shift + F
• Search Conversations: Cmd/Ctrl + F
• Export Chat: Cmd/Ctrl + E
• Settings: Cmd/Ctrl + ,