BiA-Bob#
bia_bob is a Python library that connects Jupyter with large language models (LLM) and custom bio-image analysis instructions.
Commonly, it uses OpenAIs/GPT models as default. For training purposes, we will use the LLM infrastructure of ScaDS.AI in the National Compute Center ZIH TU Dresden.
When using bia-bob to prompt LLMs, the prompts you enter including existing variable names etc. are sent to the LLM provider. Do not submit any sensitive, secret or private information. Also check bia-bob’s code recommendations before executing them. LLMs make mistakes.
First, we configure bia-bob:
# load secret API key. You must unpack the contents of api_key.zip
# into the same folder before going ahead.
from dotenv import load_dotenv
load_dotenv()
import os
from bia_bob import bob
bob.initialize(endpoint='https://llm.scads.ai/v1', model='openai/gpt-oss-120b', api_key=os.environ.get('SCADSAI_API_KEY'))
Prompting#
You can prompt for a single short task using %bob.
%bob print hello world.
The task is to output the text hello world using Python.
print("hello world")
hello world
More advanced multi-line tasks can be prompted using %%bob.
%%bob
load data/blobs.tif and show it
The task is to load an image file named “blobs.tif” from the “data” directory and display it.
from skimage.io import imread
import stackview
image = imread("data/blobs.tif")
stackview.insight(image)
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Exercise#
Ask Bob to plot a sigmoid curve.