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Microscopy Image Analysis and Quantitative Imaging Data · FreedomIntelligence | DecimalAI

Scienceby FreedomIntelligence

Microscopy Image Analysis and Quantitative Imaging Data

Production-ready microscopy image analysis and quantitative imaging data skill for colony morphometry, cell counting, fluorescence quantification, and statistical analysis of imaging-derived measurements. Processes ImageJ/CellProfiler output (area, circularity, intensity, cell counts), performs Dunnett's test, Cohen's d effect size, power analysis, Shapiro-Wilk normality tests, two-way ANOVA, polynomial regression, natural spline regression with confidence intervals, and comparative morphometry.

Never made a case worse

SkillScore

SkillScore9/100

Test results 9

Safety

3/3 safety checks passed

Code scan
Intent
Content

What it changes

5%9%of test cases passed +5 pts

Without skill1 of 22

With skill2 of 22

1 fixed1 passed either way20 still failing0 broke

Measured on gemini-3.6-flash7/26/2026v121 comparable

Track record

Agent runs: 0; All time

Use this skill

Your agent runs on

Adds every file the skill has, pinned so you can update it. No account needed.

pip install "decimalai>=0.15"
decimalai skills add tooluniverse-image-analysis
claude --plugin-dir "$(git rev-parse --show-toplevel 2>/dev/null || pwd)/.agents"

The same install from Python, for a notebook or a setup script.

Install

pip install "decimalai>=0.15"

Add the skill

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("tooluniverse-image-analysis")
if result.exit_code:
    raise SystemExit(result.problems)

print("Added. Start Claude Code with the command below.")

Start Claude Code with it

claude --plugin-dir "$(git rev-parse --show-toplevel 2>/dev/null || pwd)/.agents"

Type these in a Claude Code session. No account or API key. It writes the skill and any files it bundles, and asks first when its safety rating isn't Passed.

Add the DecimalAI plugin, once

/plugin marketplace add decimal-labs/decimalai-claude-plugins
/plugin install decimalai@decimalai

Install this skill

/decimalai:install tooluniverse-image-analysis

The plugin needs python3 and curl on your machine.

No Python or account. Claude Code picks it up in its next session.

Save it into your project

curl -fsSL --create-dirs -o .claude/skills/tooluniverse-image-analysis/SKILL.md https://app.decimal.ai/s/tooluniverse-image-analysis/SKILL.md

Copy SKILL.md

Save it in your project, as

.claude/skills/tooluniverse-image-analysis/SKILL.md

This gets SKILL.md only. The skill's 9 other files are not included.

Other ways to add it

Claude Code docs

agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.

Install

pip install "decimalai[claude-agent-sdk]"
decimalai skills add tooluniverse-image-analysis

Add it to your agent

import asyncio

from claude_agent_sdk import ClaudeAgentOptions
from decimalai.claude_agent_sdk import agent_config

# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")

async def main():
    question = "Hello!"
    async with support.run(question) as run:  # one user message, one run
        async for message in run.query(options=ClaudeAgentOptions(max_turns=6)):
            print(message)

# In a notebook or async code: await main()
asyncio.run(main())

Prefer its own loader? ClaudeAgentOptions(plugins=[skills_plugin()], skills="all") reads the same folder. Use one or the other: a skill delivered both ways reaches the prompt twice.

The same install from Python, for a notebook or a setup script. agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.

Install

pip install "decimalai[claude-agent-sdk]"

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("tooluniverse-image-analysis")
if result.exit_code:
    raise SystemExit(result.problems)

import asyncio

from claude_agent_sdk import ClaudeAgentOptions
from decimalai.claude_agent_sdk import agent_config

# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")

async def main():
    question = "Hello!"
    async with support.run(question) as run:  # one user message, one run
        async for message in run.query(options=ClaudeAgentOptions(max_turns=6)):
            print(message)

# In a notebook or async code: await main()
asyncio.run(main())

Prefer its own loader? ClaudeAgentOptions(plugins=[skills_plugin()], skills="all") reads the same folder. Use one or the other: a skill delivered both ways reaches the prompt twice.

No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.

Copy SKILL.md

Save it in your project, as

.agents/skills/tooluniverse-image-analysis/SKILL.md

Give it to your agent

import asyncio
from pathlib import Path
from claude_agent_sdk import ClaudeAgentOptions, query

skill = Path(".agents/skills/tooluniverse-image-analysis/SKILL.md").read_text()
options = ClaudeAgentOptions(system_prompt=f"You are a helpful agent.\n\n{skill}", max_turns=6)

async def main():
    async for message in query(prompt="Hello!", options=options):
        print(message)

# In a notebook or async code: await main()
asyncio.run(main())

This gets SKILL.md only. The skill's 9 other files are not included.

Other ways to add it

Claude Agent SDK docs

agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.

Install

pip install "decimalai[openai-agents]"
decimalai skills add tooluniverse-image-analysis

Add it to your agent

from agents import Agent, Runner
from decimalai.openai_agents import agent_config

# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")

agent = Agent(
    name=support.name,
    instructions=support.instructions,  # your prompt, then the skill list
    tools=[*support.tools],             # your tools, then load_skill
)
# In a notebook or async code: result = await Runner.run(agent, "Hello!")
result = Runner.run_sync(agent, "Hello!")

Using SandboxAgent? capabilities=[Shell(), decimalai.openai_agents.sandbox_skills()] points its own loader at the same folder.

Install

pip install "decimalai[openai-agents]"

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("tooluniverse-image-analysis")
if result.exit_code:
    raise SystemExit(result.problems)

from agents import Agent, Runner
from decimalai.openai_agents import agent_config

# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")

agent = Agent(
    name=support.name,
    instructions=support.instructions,  # your prompt, then the skill list
    tools=[*support.tools],             # your tools, then load_skill
)
# In a notebook or async code: result = await Runner.run(agent, "Hello!")
result = Runner.run_sync(agent, "Hello!")

Using SandboxAgent? capabilities=[Shell(), decimalai.openai_agents.sandbox_skills()] points its own loader at the same folder.

No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.

Copy SKILL.md

Save it in your project, as

.agents/skills/tooluniverse-image-analysis/SKILL.md

Give it to your agent

from pathlib import Path
from agents import Agent, Runner

skill = Path(".agents/skills/tooluniverse-image-analysis/SKILL.md").read_text()
agent = Agent(name="support", instructions=f"You are a helpful agent.\n\n{skill}")
# In a notebook or async code: result = await Runner.run(agent, "Hello!")
result = Runner.run_sync(agent, "Hello!")

This gets SKILL.md only. The skill's 9 other files are not included.

Other ways to add it

OpenAI Agents docs

agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.

Install

pip install "decimalai[openai]"
decimalai skills add tooluniverse-image-analysis

Add it to your agent

import json

from openai import OpenAI
from decimalai.openai import agent_config

client = OpenAI()
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")


def lookup_order(order_id: str) -> str:
    return f"Order {order_id} shipped yesterday."


# Your tools, as Chat Completions takes them, and what answers each.
TOOLS = [{"type": "function", "function": {
    "name": "lookup_order",
    "description": "Look up the status of an order.",
    "parameters": {"type": "object", "properties": {"order_id": {"type": "string"}},
                   "required": ["order_id"]},
}}]
FUNCTIONS = {"lookup_order": lookup_order}

question = "Where is order A1001?"
with support.run(question) as run:  # one user message, one run
    # run.system is your prompt, then the skill list.
    messages = [{"role": "system", "content": run.system}, run.message]
    while True:
        reply = client.chat.completions.create(
            model="gpt-5.4-mini",
            messages=messages,
            tools=[*TOOLS, *run.tools],  # your tools, then load_skill
        ).choices[0].message
        messages.append(reply)
        if not reply.tool_calls:
            break
        for call in reply.tool_calls:
            # load_skill is answered by the run; your own tools by FUNCTIONS.
            function = FUNCTIONS.get(call.function.name)
            messages.append(run.tool_result(call) or {
                "role": "tool", "tool_call_id": call.id,
                "content": function(**json.loads(call.function.arguments)) if function
                else f"There is no tool named {call.function.name!r}.",
            })
print(reply.content)

# The Responses API takes run.response_tools instead of run.tools.

Install

pip install "decimalai[openai]"

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("tooluniverse-image-analysis")
if result.exit_code:
    raise SystemExit(result.problems)

import json

from openai import OpenAI
from decimalai.openai import agent_config

client = OpenAI()
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")


def lookup_order(order_id: str) -> str:
    return f"Order {order_id} shipped yesterday."


# Your tools, as Chat Completions takes them, and what answers each.
TOOLS = [{"type": "function", "function": {
    "name": "lookup_order",
    "description": "Look up the status of an order.",
    "parameters": {"type": "object", "properties": {"order_id": {"type": "string"}},
                   "required": ["order_id"]},
}}]
FUNCTIONS = {"lookup_order": lookup_order}

question = "Where is order A1001?"
with support.run(question) as run:  # one user message, one run
    # run.system is your prompt, then the skill list.
    messages = [{"role": "system", "content": run.system}, run.message]
    while True:
        reply = client.chat.completions.create(
            model="gpt-5.4-mini",
            messages=messages,
            tools=[*TOOLS, *run.tools],  # your tools, then load_skill
        ).choices[0].message
        messages.append(reply)
        if not reply.tool_calls:
            break
        for call in reply.tool_calls:
            # load_skill is answered by the run; your own tools by FUNCTIONS.
            function = FUNCTIONS.get(call.function.name)
            messages.append(run.tool_result(call) or {
                "role": "tool", "tool_call_id": call.id,
                "content": function(**json.loads(call.function.arguments)) if function
                else f"There is no tool named {call.function.name!r}.",
            })
print(reply.content)

# The Responses API takes run.response_tools instead of run.tools.

No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.

Copy SKILL.md

Save it in your project, as

.agents/skills/tooluniverse-image-analysis/SKILL.md

Give it to your agent

from pathlib import Path
from openai import OpenAI

client = OpenAI()
skill = Path(".agents/skills/tooluniverse-image-analysis/SKILL.md").read_text()
reply = client.chat.completions.create(
    model="gpt-5.4-mini",
    messages=[
        {"role": "system", "content": f"You are a helpful agent.\n\n{skill}"},
        {"role": "user", "content": "Hello!"},
    ],
).choices[0].message

This gets SKILL.md only. The skill's 9 other files are not included.

Other ways to add it

OpenAI SDK docs

agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.

Install

pip install "decimalai[anthropic]"
decimalai skills add tooluniverse-image-analysis

Add it to your agent

import anthropic
from decimalai.anthropic import agent_config

client = anthropic.Anthropic()
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")

question = "Hello!"
with support.run(question) as run:  # one user message, one run
    answer = client.beta.messages.tool_runner(
        model="claude-haiku-5-5",
        max_tokens=4096,
        system=run.system,     # your prompt, then the skill list
        tools=[*run.tools],    # your tools, then load_skill
        messages=[{"role": "user", "content": question}],
    ).until_done()

Install

pip install "decimalai[anthropic]"

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("tooluniverse-image-analysis")
if result.exit_code:
    raise SystemExit(result.problems)

import anthropic
from decimalai.anthropic import agent_config

client = anthropic.Anthropic()
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")

question = "Hello!"
with support.run(question) as run:  # one user message, one run
    answer = client.beta.messages.tool_runner(
        model="claude-haiku-5-5",
        max_tokens=4096,
        system=run.system,     # your prompt, then the skill list
        tools=[*run.tools],    # your tools, then load_skill
        messages=[{"role": "user", "content": question}],
    ).until_done()

No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.

Copy SKILL.md

Save it in your project, as

.agents/skills/tooluniverse-image-analysis/SKILL.md

Give it to your agent

from pathlib import Path
import anthropic

client = anthropic.Anthropic()
skill = Path(".agents/skills/tooluniverse-image-analysis/SKILL.md").read_text()
reply = client.messages.create(
    model="claude-haiku-5-5",
    max_tokens=4096,
    system=f"You are a helpful agent.\n\n{skill}",
    messages=[{"role": "user", "content": "Hello!"}],
)

This gets SKILL.md only. The skill's 9 other files are not included.

Other ways to add it

Anthropic docs

agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.

Install

pip install "decimalai[google-genai]"
decimalai skills add tooluniverse-image-analysis

Add it to your agent

from google import genai
from google.genai import types
from decimalai.google_genai import agent_config

client = genai.Client()
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")


def lookup_order(order_id: str) -> str:
    return f"Order {order_id} shipped yesterday."


# Your functions, as declarations for the model, and what answers each.
TOOLS = [{"function_declarations": [{
    "name": "lookup_order",
    "description": "Look up the status of an order.",
    "parameters_json_schema": {"type": "object", "properties": {"order_id": {"type": "string"}},
                               "required": ["order_id"]},
}]}]
FUNCTIONS = {"lookup_order": lookup_order}

question = "Where is order A1001?"
with support.run(question) as run:  # one user message, one run
    config = types.GenerateContentConfig(
        system_instruction=run.system,     # your prompt, then the skill list
        tools=[*TOOLS, *run.tool_params],  # your functions, then load_skill
    )
    contents = [{"role": "user", "parts": [{"text": run.message}]}]
    while True:
        response = client.models.generate_content(
            model="gemini-3.5-flash", contents=contents, config=config,
        )
        if not response.function_calls:
            break
        contents.append(response.candidates[0].content)
        parts = []
        for call in response.function_calls:
            # load_skill is answered by the run; your own functions by FUNCTIONS.
            # A loop of your own rather than automatic function calling, which
            # raises KeyError when the model asks for a function you did not pass.
            function = FUNCTIONS.get(call.name)
            parts.append(run.tool_result(call) or {"function_response": {
                "name": call.name, "id": call.id,
                "response": {"result": function(**(call.args or {})) if function
                             else f"There is no function named {call.name!r}."},
            }})
        contents.append({"role": "user", "parts": parts})
print(response.text)

Install

pip install "decimalai[google-genai]"

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("tooluniverse-image-analysis")
if result.exit_code:
    raise SystemExit(result.problems)

from google import genai
from google.genai import types
from decimalai.google_genai import agent_config

client = genai.Client()
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")


def lookup_order(order_id: str) -> str:
    return f"Order {order_id} shipped yesterday."


# Your functions, as declarations for the model, and what answers each.
TOOLS = [{"function_declarations": [{
    "name": "lookup_order",
    "description": "Look up the status of an order.",
    "parameters_json_schema": {"type": "object", "properties": {"order_id": {"type": "string"}},
                               "required": ["order_id"]},
}]}]
FUNCTIONS = {"lookup_order": lookup_order}

question = "Where is order A1001?"
with support.run(question) as run:  # one user message, one run
    config = types.GenerateContentConfig(
        system_instruction=run.system,     # your prompt, then the skill list
        tools=[*TOOLS, *run.tool_params],  # your functions, then load_skill
    )
    contents = [{"role": "user", "parts": [{"text": run.message}]}]
    while True:
        response = client.models.generate_content(
            model="gemini-3.5-flash", contents=contents, config=config,
        )
        if not response.function_calls:
            break
        contents.append(response.candidates[0].content)
        parts = []
        for call in response.function_calls:
            # load_skill is answered by the run; your own functions by FUNCTIONS.
            # A loop of your own rather than automatic function calling, which
            # raises KeyError when the model asks for a function you did not pass.
            function = FUNCTIONS.get(call.name)
            parts.append(run.tool_result(call) or {"function_response": {
                "name": call.name, "id": call.id,
                "response": {"result": function(**(call.args or {})) if function
                             else f"There is no function named {call.name!r}."},
            }})
        contents.append({"role": "user", "parts": parts})
print(response.text)

No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.

Copy SKILL.md

Save it in your project, as

.agents/skills/tooluniverse-image-analysis/SKILL.md

Give it to your agent

from pathlib import Path
from google import genai
from google.genai import types

client = genai.Client()
skill = Path(".agents/skills/tooluniverse-image-analysis/SKILL.md").read_text()
response = client.models.generate_content(
    model="gemini-3.5-flash",
    contents="Hello!",
    config=types.GenerateContentConfig(system_instruction=f"You are a helpful agent.\n\n{skill}"),
)

This gets SKILL.md only. The skill's 9 other files are not included.

Other ways to add it

Gemini API docs

agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.

Install

pip install "decimalai[langchain]" langchain-openai
decimalai skills add tooluniverse-image-analysis

Add it to your agent

from langchain.agents import create_agent
from decimalai.langchain import agent_config

# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")

agent = create_agent(
    "openai:gpt-5.4-mini",
    tools=[],                         # your tools; the middleware adds load_skill
    middleware=[support.middleware],  # your prompt, the skill list and load_skill
)
result = agent.invoke({"messages": [{"role": "user", "content": "Hello!"}]})

Install

pip install "decimalai[langchain]" langchain-openai

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("tooluniverse-image-analysis")
if result.exit_code:
    raise SystemExit(result.problems)

from langchain.agents import create_agent
from decimalai.langchain import agent_config

# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")

agent = create_agent(
    "openai:gpt-5.4-mini",
    tools=[],                         # your tools; the middleware adds load_skill
    middleware=[support.middleware],  # your prompt, the skill list and load_skill
)
result = agent.invoke({"messages": [{"role": "user", "content": "Hello!"}]})

No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.

Copy SKILL.md

Save it in your project, as

.agents/skills/tooluniverse-image-analysis/SKILL.md

Give it to your agent

from pathlib import Path
from langchain.agents import create_agent

skill = Path(".agents/skills/tooluniverse-image-analysis/SKILL.md").read_text()
agent = create_agent("openai:gpt-5.4-mini", tools=[], system_prompt=f"You are a helpful agent.\n\n{skill}")
result = agent.invoke({"messages": [{"role": "user", "content": "Hello!"}]})

This gets SKILL.md only. The skill's 9 other files are not included.

Other ways to add it

LangChain docs

CrewAI's own skill loader reads the installed folder. No DecimalAI account needed.

Install

pip install "decimalai>=0.16" "crewai>=1.15.27"
decimalai skills add tooluniverse-image-analysis

Add it to your agent

import decimalai.crewai
from crewai import Agent, Crew, Task

agent = Agent(
    role="Support", goal="Help the customer", backstory="A support agent.",
    llm=llm,                               # your own CrewAI LLM
    skills=decimalai.crewai.skills(),      # the installed folder
    tools=decimalai.crewai.skill_tools(),  # reads a skill's files, runs its scripts
)
task = Task(description="Hello!", expected_output="an answer", agent=agent)
Crew(agents=[agent], tasks=[task]).kickoff()

The same install from Python, for a notebook or a setup script. CrewAI's own skill loader reads the installed folder. No DecimalAI account needed.

Install

pip install "decimalai>=0.16" "crewai>=1.15.27"

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("tooluniverse-image-analysis")
if result.exit_code:
    raise SystemExit(result.problems)

import decimalai.crewai
from crewai import Agent, Crew, Task

agent = Agent(
    role="Support", goal="Help the customer", backstory="A support agent.",
    llm=llm,                               # your own CrewAI LLM
    skills=decimalai.crewai.skills(),      # the installed folder
    tools=decimalai.crewai.skill_tools(),  # reads a skill's files, runs its scripts
)
task = Task(description="Hello!", expected_output="an answer", agent=agent)
Crew(agents=[agent], tasks=[task]).kickoff()

No DecimalAI package. CrewAI's own loader reads the folder, and nothing pins or updates it.

Copy SKILL.md

Save it in your project, as

.agents/skills/tooluniverse-image-analysis/SKILL.md

Give it to your agent

from pathlib import Path
from crewai import Agent, Crew, Task

agent = Agent(
    role="Support", goal="Help the customer", backstory="A support agent.",
    llm=llm,                         # your own CrewAI LLM
    skills=[Path(".agents/skills")],
)
task = Task(description="Hello!", expected_output="an answer", agent=agent)
Crew(agents=[agent], tasks=[task]).kickoff()

This gets SKILL.md only. The skill's 9 other files are not included.

Other ways to add it

CrewAI docs

agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.

Install

pip install "decimalai[adk]"
decimalai skills add tooluniverse-image-analysis

Add it to your agent

from decimalai.adk import DecimalAIPlugin, agent_config
from google.adk.agents import LlmAgent
from google.adk.apps import App

# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")

agent = LlmAgent(
    name="support",          # ADK needs a Python identifier
    model="gemini-3.5-flash",
    instruction=support.instruction,  # your prompt, then the skill list
    tools=[*support.tools],           # your tools, then load_skill
)
# DecimalAIPlugin makes each invocation of runners built from this App one trace.
app = App(name="support", root_agent=agent, plugins=[DecimalAIPlugin()])

Prefer ADK's own loader? SkillToolset(skills=decimalai.adk.skills(), ...) reads the same folder. Use one or the other: a skill delivered both ways reaches the prompt twice.

Install

pip install "decimalai[adk]"

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("tooluniverse-image-analysis")
if result.exit_code:
    raise SystemExit(result.problems)

from decimalai.adk import DecimalAIPlugin, agent_config
from google.adk.agents import LlmAgent
from google.adk.apps import App

# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")

agent = LlmAgent(
    name="support",          # ADK needs a Python identifier
    model="gemini-3.5-flash",
    instruction=support.instruction,  # your prompt, then the skill list
    tools=[*support.tools],           # your tools, then load_skill
)
# DecimalAIPlugin makes each invocation of runners built from this App one trace.
app = App(name="support", root_agent=agent, plugins=[DecimalAIPlugin()])

Prefer ADK's own loader? SkillToolset(skills=decimalai.adk.skills(), ...) reads the same folder. Use one or the other: a skill delivered both ways reaches the prompt twice.

No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.

Copy SKILL.md

Save it in your project, as

.agents/skills/tooluniverse-image-analysis/SKILL.md

Give it to your agent

from pathlib import Path
from google.adk.agents import LlmAgent

skill = Path(".agents/skills/tooluniverse-image-analysis/SKILL.md").read_text()
agent = LlmAgent(
    name="support",
    model="gemini-3.5-flash",
    instruction=lambda context: f"You are a helpful agent.\n\n{skill}",
)

This gets SKILL.md only. The skill's 9 other files are not included.

Other ways to add it

Google ADK docs

agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.

Install

pip install "decimalai[pydantic-ai]"
decimalai skills add tooluniverse-image-analysis

Add it to your agent

from pydantic_ai import Agent
from decimalai.pydantic_ai import agent_config

# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")

agent = Agent(
    "openai:gpt-4o-mini",
    name=support.name,
    tools=[],                 # your tools; the capability adds load_skill
    capabilities=[support],   # your prompt, the skill list and load_skill
)
# In a notebook or async code: result = await agent.run("Hello!")
result = agent.run_sync("Hello!")

On the Pydantic AI harness, decimalai.pydantic_ai_harness.skills(project) uses its own loader instead.

Install

pip install "decimalai[pydantic-ai]"

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("tooluniverse-image-analysis")
if result.exit_code:
    raise SystemExit(result.problems)

from pydantic_ai import Agent
from decimalai.pydantic_ai import agent_config

# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")

agent = Agent(
    "openai:gpt-4o-mini",
    name=support.name,
    tools=[],                 # your tools; the capability adds load_skill
    capabilities=[support],   # your prompt, the skill list and load_skill
)
# In a notebook or async code: result = await agent.run("Hello!")
result = agent.run_sync("Hello!")

On the Pydantic AI harness, decimalai.pydantic_ai_harness.skills(project) uses its own loader instead.

No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.

Copy SKILL.md

Save it in your project, as

.agents/skills/tooluniverse-image-analysis/SKILL.md

Give it to your agent

from pathlib import Path
from pydantic_ai import Agent

skill = Path(".agents/skills/tooluniverse-image-analysis/SKILL.md").read_text()
agent = Agent("openai:gpt-4o-mini", instructions=f"You are a helpful agent.\n\n{skill}")
# In a notebook or async code: result = await agent.run("Hello!")
result = agent.run_sync("Hello!")

This gets SKILL.md only. The skill's 9 other files are not included.

Other ways to add it

Pydantic AI docs

Deep Agents' own skill loader reads the installed folder. No DecimalAI account needed.

Install

pip install "decimalai>=0.16" deepagents
decimalai skills add tooluniverse-image-analysis

Add it to your agent

import decimalai.deepagents
from deepagents import create_deep_agent

agent = create_deep_agent(model=model, **decimalai.deepagents.skills())
agent.invoke({"messages": [{"role": "user", "content": "Hello!"}]})

The default backend reads files but has no shell. To run a skill's scripts, pass skills(backend=LocalShellBackend(...)).

The same install from Python, for a notebook or a setup script. Deep Agents' own skill loader reads the installed folder. No DecimalAI account needed.

Install

pip install "decimalai>=0.16" deepagents

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("tooluniverse-image-analysis")
if result.exit_code:
    raise SystemExit(result.problems)

import decimalai.deepagents
from deepagents import create_deep_agent

agent = create_deep_agent(model=model, **decimalai.deepagents.skills())
agent.invoke({"messages": [{"role": "user", "content": "Hello!"}]})

The default backend reads files but has no shell. To run a skill's scripts, pass skills(backend=LocalShellBackend(...)).

No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.

Copy SKILL.md

Save it in your project, as

.agents/skills/tooluniverse-image-analysis/SKILL.md

Give it to your agent

from pathlib import Path
from deepagents import create_deep_agent

skill = Path(".agents/skills/tooluniverse-image-analysis/SKILL.md").read_text()
agent = create_deep_agent(model=model, system_prompt=f"You are a helpful agent.\n\n{skill}")
agent.invoke({"messages": [{"role": "user", "content": "Hello!"}]})

This gets SKILL.md only. The skill's 9 other files are not included.

Other ways to add it

Deep Agents docs

Its own skill loader reads the installed folder. No DecimalAI account needed.

Install

pip install "decimalai>=0.16" agent-framework
decimalai skills add tooluniverse-image-analysis

Add it to your agent

import asyncio

from agent_framework import Agent
from decimalai.agent_framework import skills

agent = Agent(client=client, instructions="You are a helpful agent.", context_providers=[skills()])
asyncio.run(agent.run("Hello!"))

It caches skills by default, so restart the process after decimalai skills update.

The same install from Python, for a notebook or a setup script. Its own skill loader reads the installed folder. No DecimalAI account needed.

Install

pip install "decimalai>=0.16" agent-framework

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("tooluniverse-image-analysis")
if result.exit_code:
    raise SystemExit(result.problems)

import asyncio

from agent_framework import Agent
from decimalai.agent_framework import skills

agent = Agent(client=client, instructions="You are a helpful agent.", context_providers=[skills()])
asyncio.run(agent.run("Hello!"))

It caches skills by default, so restart the process after decimalai skills update.

No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.

Copy SKILL.md

Save it in your project, as

.agents/skills/tooluniverse-image-analysis/SKILL.md

Give it to your agent

import asyncio
from pathlib import Path
from agent_framework import Agent

skill = Path(".agents/skills/tooluniverse-image-analysis/SKILL.md").read_text()
agent = Agent(client=client, instructions=f"You are a helpful agent.\n\n{skill}")
asyncio.run(agent.run("Hello!"))

This gets SKILL.md only. The skill's 9 other files are not included.

Other ways to add it

Microsoft Agent Framework docs

Strands' own skill loader reads the installed folder. No DecimalAI account needed.

Install

pip install "decimalai>=0.16" strands-agents
decimalai skills add tooluniverse-image-analysis

Add it to your agent

from decimalai.strands import skills
from strands import Agent
from strands.vended_tools import file_editor, shell

agent = Agent(
    model=model,                # always pass one: the default is Amazon Bedrock
    system_prompt="You are a helpful agent.",
    tools=[file_editor, shell],
    plugins=[skills()],
)
agent("Hello!")

Strands loads an agent's skills once, so build the agent again after decimalai skills update.

The same install from Python, for a notebook or a setup script. Strands' own skill loader reads the installed folder. No DecimalAI account needed.

Install

pip install "decimalai>=0.16" strands-agents

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("tooluniverse-image-analysis")
if result.exit_code:
    raise SystemExit(result.problems)

from decimalai.strands import skills
from strands import Agent
from strands.vended_tools import file_editor, shell

agent = Agent(
    model=model,                # always pass one: the default is Amazon Bedrock
    system_prompt="You are a helpful agent.",
    tools=[file_editor, shell],
    plugins=[skills()],
)
agent("Hello!")

Strands loads an agent's skills once, so build the agent again after decimalai skills update.

No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.

Copy SKILL.md

Save it in your project, as

.agents/skills/tooluniverse-image-analysis/SKILL.md

Give it to your agent

from pathlib import Path
from strands import Agent

skill = Path(".agents/skills/tooluniverse-image-analysis/SKILL.md").read_text()
agent = Agent(model=model, system_prompt=f"You are a helpful agent.\n\n{skill}")
agent("Hello!")

This gets SKILL.md only. The skill's 9 other files are not included.

Other ways to add it

Strands docs

Adds every file the skill has, pinned so you can update it. Cursor, Copilot, Cline and Warp read this folder by themselves.

pip install "decimalai>=0.15"
decimalai skills add tooluniverse-image-analysis

No Python or account. Cursor, Copilot, Cline and Warp read this folder by themselves.

Save it into your project

curl -fsSL --create-dirs -o .agents/skills/tooluniverse-image-analysis/SKILL.md https://app.decimal.ai/s/tooluniverse-image-analysis/SKILL.md

Copy SKILL.md

Save it in your project, as

.agents/skills/tooluniverse-image-analysis/SKILL.md

This gets SKILL.md only. The skill's 9 other files are not included.

Other ways to add it

Cursor and other editors docs

Fetch the file and give its text to your model as instructions. No account or package needed.

Get the file

curl -fsSL https://app.decimal.ai/s/tooluniverse-image-analysis/SKILL.md

Read the summary as JSON

curl -fsSL https://app.decimal.ai/s/tooluniverse-image-analysis.json

This gets SKILL.md only. The skill's 9 other files are not included.

Other ways to add it

Other setups docs

You don't need a DecimalAI account.

Version: v1, tested 7/26/2026
Source: FreedomIntelligence/OpenClaw-Medical-Skills ↗
License: Not recorded

Manage it in DecimalAI

Saved prompts and skills, pinned versions, and traces of this skill in your runs. DecimalAI does not run your agent.

Claude Code reads files from your project, so DecimalAI config does not apply there.

On Claude Agent SDK: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.

On OpenAI Agents: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.

On OpenAI SDK: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.

On Anthropic: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.

On Gemini API: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.

On LangChain: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.

On CrewAI: set DECIMAL_API_KEY and add decimalai.init(crewai=True) to record runs and skill use. The skill version stays in your repo.

On Google ADK: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.

On Pydantic AI: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.

On Deep Agents: set DECIMAL_API_KEY and add decimalai.init(langchain=True) to record runs and skill use. The skill version stays in your repo.

On Microsoft Agent Framework: set DECIMAL_API_KEY and add decimalai.init(otel=True, agent_name="support") to record runs and skill use. The skill version stays in your repo.

On Strands: set DECIMAL_API_KEY and add decimalai.init(otel=True, agent_name="support") to record runs and skill use. The skill version stays in your repo.

Editors read files from your project, so DecimalAI config does not apply there.

Anywhere else: record a use with decimalai.log_skill_activation() inside a trace.

Use this skill

SKILL.md

Microscopy Image Analysis and Quantitative Imaging Data

Production-ready skill for analyzing microscopy-derived measurement data using pandas, numpy, scipy, statsmodels, and scikit-image. Designed for BixBench imaging questions covering colony morphometry, cell counting, fluorescence quantification, regression modeling, and statistical comparisons.

IMPORTANT: This skill handles complex multi-workflow analysis. Most implementation details have been moved to references/ for progressive disclosure. This document focuses on high-level decision-making and workflow orchestration.

When to Use This Skill

Apply when users:

Have microscopy measurement data (area, circularity, intensity, cell counts) in CSV/TSV
Ask about colony morphometry (bacterial swarming, biofilm, growth assays)
Need statistical comparisons of imaging measurements (t-test, ANOVA, Dunnett's, Mann-Whitney)
Ask about cell counting statistics (NeuN, DAPI, marker counts)
Need effect size calculations (Cohen's d) and power analysis
Want regression models (polynomial, spline) fitted to dose-response or ratio data
Ask about model comparison (R-squared, F-statistic, AIC/BIC)
Need Shapiro-Wilk normality testing on imaging data
Want confidence intervals for peak predictions from fitted models
Questions mention imaging software output (ImageJ, CellProfiler, QuPath)
Need fluorescence intensity quantification or colocalization analysis
Ask about image segmentation results (counts, areas, shapes)

BixBench Coverage: 21 questions across 4 projects (bix-18, bix-19, bix-41, bix-54)

NOT for (use other skills instead):

Phylogenetic analysis → Use tooluniverse-phylogenetics
RNA-seq differential expression → Use tooluniverse-rnaseq-deseq2
Single-cell scRNA-seq → Use tooluniverse-single-cell
Statistical regression only (no imaging context) → Use tooluniverse-statistical-modeling

Core Principles

Data-first approach - Load and inspect all CSV/TSV measurement data before analysis
Question-driven - Parse the exact statistic, comparison, or model requested
Statistical rigor - Proper effect sizes, multiple comparison corrections, model selection
Imaging-aware - Understand ImageJ/CellProfiler measurement columns (Area, Circularity, Round, Intensity)
Workflow flexibility - Support both pre-quantified data (CSV) and raw image processing
Precision - Match expected answer format (integer, range, decimal places)
Reproducible - Use standard Python/scipy equivalents to R functions

Required Python Packages

# Core (MUST be installed)
import pandas as pd
import numpy as np
from scipy import stats
from scipy.interpolate import BSpline, make_interp_spline
import statsmodels.api as sm
from statsmodels.formula.api import ols
from statsmodels.stats.power import TTestIndPower
from patsy import dmatrix, bs, cr

# Optional (for raw image processing)
import skimage
import cv2
import tifffile

Installation:

pip install pandas numpy scipy statsmodels patsy scikit-image opencv-python-headless tifffile

High-Level Workflow Decision Tree

START: User question about microscopy data
│
├─ Q1: What type of data is available?
│  │
│  ├─ PRE-QUANTIFIED DATA (CSV/TSV with measurements)
│  │  └─ Workflow: Load → Parse question → Statistical analysis
│  │     Pattern: Most common BixBench pattern (bix-18, bix-19, bix-41, bix-54)
│  │     See: Section "Quantitative Data Analysis" below
│  │
│  └─ RAW IMAGES (TIFF, PNG, multi-channel)
│     └─ Workflow: Load → Segment → Measure → Analyze
│        See: references/image_processing.md
│
├─ Q2: What type of analysis is needed?
│  │
│  ├─ STATISTICAL COMPARISON
│  │  ├─ Two groups → t-test or Mann-Whitney
│  │  ├─ Multiple groups → ANOVA or Dunnett's test
│  │  ├─ Two factors → Two-way ANOVA
│  │  └─ Effect size → Cohen's d, power analysis
│  │  See: references/statistical_analysis.md
│  │
│  ├─ REGRESSION MODELING
│  │  ├─ Dose-response → Polynomial (quadratic, cubic)
│  │  ├─ Ratio optimization → Natural spline
│  │  └─ Model comparison → R-squared, F-statistic, AIC/BIC
│  │  See: references/statistical_analysis.md
│  │
│  ├─ CELL COUNTING
│  │  ├─ Fluorescence (DAPI, NeuN) → Threshold + watershed
│  │  ├─ Brightfield → Adaptive threshold
│  │  └─ High-density → CellPose or StarDist (external)
│  │  See: references/cell_counting.md
│  │
│  ├─ COLONY SEGMENTATION
│  │  ├─ Swarming assays → Otsu threshold + morphology
│  │  ├─ Biofilms → Li threshold + fill holes
│  │  └─ Growth assays → Time-lapse tracking
│  │  See: references/segmentation.md
│  │
│  └─ FLUORESCENCE QUANTIFICATION
│     ├─ Intensity measurement → regionprops
│     ├─ Colocalization → Pearson/Manders
│     └─ Multi-channel → Channel-wise quantification
│     See: references/fluorescence_analysis.md
│
└─ Q3: When to use scikit-image vs OpenCV?
   ├─ scikit-image: Scientific analysis, measurements, regionprops
   ├─ OpenCV: Fast processing, real-time, large batches
   └─ Both: Often interchangeable for basic operations
   See: references/image_processing.md "Library Selection Guide"

Quantitative Data Analysis Workflow

Phase 0: Question Parsing and Data Discovery

CRITICAL FIRST STEP: Before writing ANY code, identify what data files are available and what the question is asking for.

import os, glob, pandas as pd

# Discover data files
data_dir = "."
csv_files = glob.glob(os.path.join(data_dir, '**', '*.csv'), recursive=True)
tsv_files = glob.glob(os.path.join(data_dir, '**', '*.tsv'), recursive=True)
img_files = glob.glob(os.path.join(data_dir, '**', '*.tif*'), recursive=True)

# Load and inspect first measurement file
if csv_files:
    df = pd.read_csv(csv_files[0])
    print(f"Shape: {df.shape}")
    print(f"Columns: {list(df.columns)}")
    print(df.head())
    print(df.describe())

Common Column Names:

Area: Colony or cell area in pixels or calibrated units
Circularity: 4piarea/perimeter^2, range [0,1], 1.0 = perfect circle
Round: Roundness = 4area/(pimajor_axis^2)
Genotype/Strain: Biological grouping variable
Ratio: Co-culture mixing ratio (e.g., "1:3", "5:1")
NeuN/DAPI/GFP: Cell marker counts or intensities

Phase 1: Grouped Statistics

def grouped_summary(df, group_cols, measure_col):
    """Calculate summary statistics by group."""
    summary = df.groupby(group_cols)[measure_col].agg(
        Mean='mean',
        SD='std',
        Median='median',
        Min='min',
        Max='max',
        N='count'
    ).reset_index()
    summary['SEM'] = summary['SD'] / np.sqrt(summary['N'])
    return summary

# Example: Colony morphometry by genotype
area_summary = grouped_summary(df, 'Genotype', 'Area')
circ_summary = grouped_summary(df, 'Genotype', 'Circularity')

For detailed statistical functions, see: references/statistical_analysis.md

Phase 2: Statistical Testing

Decision guide:

Normality test needed? → Shapiro-Wilk
Two groups comparison? → t-test or Mann-Whitney
Multiple groups vs control? → Dunnett's test
Multiple groups, all comparisons? → Tukey HSD
Two factors? → Two-way ANOVA
Effect size? → Cohen's d
Sample size planning? → Power analysis

See: references/statistical_analysis.md for complete implementations

Phase 3: Regression Modeling

When to use each model:

Polynomial (quadratic/cubic): Smooth dose-response, clear peak
Natural spline: Flexible, non-parametric, handles complex patterns
Linear: Simple relationships, checking for trends

Model comparison metrics:

R-squared: Overall fit (higher = better)
Adjusted R-squared: Penalizes complexity
F-statistic p-value: Model significance
AIC/BIC: Compare non-nested models

See: references/statistical_analysis.md for complete implementations

Raw Image Processing Workflow

When Processing Raw Images

Workflow: Load → Preprocess → Segment → Measure → Export

# Quick start for cell counting
from scripts.segment_cells import count_cells_in_image

result = count_cells_in_image(
    image_path="cells.tif",
    channel=0,  # DAPI channel
    min_area=50
)
print(f"Found {result['count']} cells")

Segmentation Method Selection

Decision guide:

Cell Type	Density	Best Method	Notes
Nuclei (DAPI)	Low-Medium	Otsu + watershed	Standard approach
Nuclei (DAPI)	High	CellPose/StarDist	Handles touching
Colonies	Well-separated	Otsu threshold	Fast, reliable
Colonies	Touching	Watershed	Edge detection
Cells (phase)	Any	Adaptive threshold	Handles uneven illumination
Fluorescence	Low signal	Li threshold	More sensitive

See: references/segmentation.md and references/cell_counting.md for detailed protocols

Library Selection: scikit-image vs OpenCV

Use scikit-image when:

Scientific measurements needed (area, perimeter, intensity)
regionprops for object properties
Publication-quality analysis
Easier syntax for scientists

Use OpenCV when:

Processing large image batches
Speed is critical
Real-time processing
Advanced computer vision features

Both work for:

Thresholding, filtering, morphological operations
Basic image transformations
Most segmentation tasks

See: references/image_processing.md "Library Selection Guide"

Common BixBench Patterns

Pattern 1: Colony Morphometry (bix-18)

Question type: "Mean circularity of genotype with largest area?"

Data: CSV with Genotype, Area, Circularity columns

Workflow:

Load CSV → group by Genotype
Calculate mean Area per genotype
Identify genotype with max mean Area
Report mean Circularity for that genotype

See: references/segmentation.md "Colony Morphometry Analysis"

Pattern 2: Cell Counting Statistics (bix-19)

Question type: "Cohen's d for NeuN counts between conditions?"

Data: CSV with Condition, NeuN_count, Sex, Hemisphere columns

Workflow:

Load CSV → filter by hemisphere/sex if needed
Split by Condition (KD vs CTRL)
Calculate Cohen's d with pooled SD
Report effect size

See: references/statistical_analysis.md "Effect Size Calculations"

Pattern 3: Multi-Group Comparison (bix-41)

Question type: "Dunnett's test: How many ratios equivalent to control?"

Data: CSV with multiple co-culture ratios, Area, Circularity

Workflow:

Create Strain_Ratio labels
Run Dunnett's test for Area (vs control)
Run Dunnett's test for Circularity (vs control)
Count groups NOT significant in BOTH tests

See: references/statistical_analysis.md "Dunnett's Test"

Pattern 4: Regression Optimization (bix-54)

Question type: "Peak frequency from natural spline model?"

Data: CSV with co-culture frequencies and Area measurements

Workflow:

Convert ratio strings to frequencies
Fit natural spline model (df=4)
Find peak via grid search
Report peak frequency + confidence interval

See: references/statistical_analysis.md "Regression Modeling"

Quick Reference Table

Task	Primary Tool	Reference
Load measurement CSV	pandas.read_csv()	This file
Group statistics	df.groupby().agg()	This file
T-test	scipy.stats.ttest_ind()	statistical_analysis.md
ANOVA	statsmodels.ols + anova_lm()	statistical_analysis.md
Dunnett's test	scipy.stats.dunnett()	statistical_analysis.md
Cohen's d	Custom function (pooled SD)	statistical_analysis.md
Power analysis	statsmodels TTestIndPower	statistical_analysis.md
Polynomial regression	statsmodels.OLS + poly features	statistical_analysis.md
Natural spline	patsy.cr() + statsmodels.OLS	statistical_analysis.md
Cell segmentation	skimage.filters + watershed	cell_counting.md
Colony segmentation	skimage.filters.threshold_otsu	segmentation.md
Fluorescence quantification	skimage.measure.regionprops	fluorescence_analysis.md
Colocalization	Pearson/Manders	fluorescence_analysis.md
Image loading	tifffile, skimage.io	image_processing.md
Batch processing	scripts/batch_process.py	scripts/

Example Scripts

Ready-to-use scripts in scripts/ directory:

segment_cells.py - Cell/nuclei counting with watershed
measure_fluorescence.py - Multi-channel intensity quantification
batch_process.py - Process folders of images
colony_morphometry.py - Measure colony area/circularity
statistical_comparison.py - Group comparison statistics

Usage:

# Count cells in image
python scripts/segment_cells.py cells.tif --channel 0 --min-area 50

# Batch process folder
python scripts/batch_process.py input_folder/ output.csv --analysis cell_count

Detailed Reference Guides

For complete implementations and protocols:

references/statistical_analysis.md - All statistical tests, regression models
references/cell_counting.md - Cell/nuclei counting protocols
references/segmentation.md - Colony and object segmentation
references/fluorescence_analysis.md - Intensity quantification, colocalization
references/image_processing.md - Image loading, preprocessing, library selection
references/troubleshooting.md - Common issues and solutions

Important Notes

Matching R Statistical Functions

Some BixBench questions use R for analysis. Python equivalents:

R's Dunnett test (multcomp::glht) → scipy.stats.dunnett() (scipy ≥ 1.10)
R's natural spline (ns(x, df=4)) → patsy.cr(x, knots=...) with explicit quantile knots
R's t-test (t.test()) → scipy.stats.ttest_ind()
R's ANOVA (aov()) → statsmodels.formula.api.ols() + sm.stats.anova_lm()

See: references/statistical_analysis.md for exact parameter matching

Answer Formatting

BixBench expects specific formats:

"to the nearest thousand": int(round(val, -3))
Percentages: Usually integer or 1-2 decimal places
Cohen's d: 3 decimal places
Sample sizes: Always integer (ceiling)
Ratios: String format "5:1"

Completeness Checklist

Before returning your answer, verify:

Loaded all data files and inspected column names
Identified the specific statistic or model requested
Used correct grouping variables and filter conditions
Applied correct rounding or format
For "how many" questions: counted correctly based on criteria
For statistical tests: used appropriate multiple comparison correction
For regression: properly prepared and transformed data
Double-checked direction of comparisons
Verified answer falls within expected range

Getting Help

Start with decision tree at top of this file
Check relevant reference guide for detailed protocol
Use example scripts as templates
See troubleshooting guide for common issues
All statistical implementations in statistical_analysis.md

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Source

Imported

FreedomIntelligence / OpenClaw-Medical-Skills

skills/tooluniverse-image-analysis/SKILL.md

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Imported 8/1/2026Version v1Bundled 9 files · scripts

Illustrative Want to see what tooluniverse-image-analysis would put in front of your model? Preview the rendered body and check its trigger phrases — no LLM call, no signup.

Other skills for the same job

Published skills whose descriptions closely match this one, with their headline benchmark lift.

mims-harvard/tooluniverse-image-analysisMicroscopy and quantitative imaging analysis — colony morphometry, fluorescence intensity quantification, cell-count statistics, dose-response curves, and ANOVA/Dunnett on image-derived measurements. Uses pandas/numpy/scipy/scikit-image. Use for analyzing tabular outputs from CellProfiler/ImageJ, image-derived measurement statistics, and image-based assay quantification.Close match-9 pts pass-rate lift

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Microscopy Image Analysis and Quantitative Imaging Data

When to Use This Skill

Core Principles

Required Python Packages

High-Level Workflow Decision Tree

Quantitative Data Analysis Workflow

Phase 0: Question Parsing and Data Discovery

Phase 1: Grouped Statistics

Phase 2: Statistical Testing

Phase 3: Regression Modeling

Raw Image Processing Workflow

When Processing Raw Images

Segmentation Method Selection

Library Selection: scikit-image vs OpenCV

Common BixBench Patterns

Pattern 1: Colony Morphometry (bix-18)

Pattern 2: Cell Counting Statistics (bix-19)

Pattern 3: Multi-Group Comparison (bix-41)

Pattern 4: Regression Optimization (bix-54)

Quick Reference Table

Example Scripts

Detailed Reference Guides

Important Notes

Matching R Statistical Functions

Answer Formatting

Completeness Checklist

Getting Help

SkillSafety

Source

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