bia-bob 0.2.2

A Jupyter-based assistant for working on bio-image analysis tasks

bia-bob

BIA Bob is a Jupyter-based assistant for interacting with image data and for working on Bio-image Analysis tasks. It is based on LangChain and OpenAI's API. You need an openai API account to use it.

Trailer:

Note: Bob is currently in an early alpha stage. It is not very smart yet and only knows some basic image processing algorithms. Feedback and contributions are very welcome!

Usage

You can initialize Bob like this:

from bia_bob import bob

In case you want it to be aware of all your variables, call this additionally:

bob.initialize(globals())

Afterwards, you can ask Bob questions like this:

%bob Load blobs.tif and show it

Or like this:

%%bob
Please load the image blobs.tif,
segment bright objects in it, 
count them and 
show the segmentation result.

You can also ask Bob about available tools:

%bob list tools

Detailed examples of how to interact with Bob are given in these notebooks:

• Basic usage
• Speech recognition
• Complete Bio-image Analysis Workflow
• Accessing variables
• Image Filtering
• Choosing image segmentation algorithms
• Asking Bob what it does
• Listing tools
• Browsing folders
• Interactive image stack viewing
• For developers
• Extensibility

Example gallery

Known issues

If you want to ask Bob a question, you need to put a space before the ?.

What do you know about blobs.gif ?

Installation

pip install bia-bob

Issues

If you encounter any problems or want to provide feedback or suggestions, please create a thread on image.sc along with a detailed description and tag [@haesleinhuepf].