A Jupyter-based assistant for working on bio-image analysis tasks
Project description
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].
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.