Metadata-Version: 2.4
Name: biopb
Version: 0.5.4
Summary: Python bindings of BioPB: open protobuf/gRPC protocols for biomedical image processing
Author-email: Ji Yu <jyu@uchc.edu>
License-Expression: MIT
Project-URL: Homepage, https://github.com/biopb/biopb
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: protobuf>=6.32.1
Requires-Dist: grpcio
Requires-Dist: numpy
Requires-Dist: typer[all]>=0.9.0
Requires-Dist: imageio
Provides-Extra: test
Requires-Dist: pytest>=7.0; extra == "test"
Requires-Dist: opencv-python-headless==4.10.0.84; extra == "test"
Provides-Extra: tensor
Requires-Dist: pyarrow>=14.0.0; extra == "tensor"
Requires-Dist: dask[array]>=2024.0.0; extra == "tensor"
Requires-Dist: cachey>=0.1.0; extra == "tensor"
Requires-Dist: ome-zarr>=0.6.1; extra == "tensor"
Requires-Dist: aicsimageio>=4.14.0; extra == "tensor"
Dynamic: license-file

# BioPB

_Distributed computing for bio-imaging data._

BioPB provides a standardized way to share multi-dimensional microscopy datasets, analysis algorithms, and computational results in a network-transparent and language-agnostic manner. 

## Biopb-Tensor

A blazing-fast microscopy data server for sharing your lab's petabyte-scale datasets to team members and/or collaborators. [Read More...](biopb-tensor-server/README.md)

  - **Uniform Representation**: all source data mapped to a _multi-resolution_ and _lazy-read_ array for client access
  - **Multi-language**: dask array for Python and ImgLib2.CellImg for Java
  - **Thread-safe & Serializable**: compatible with dask.distribute for distributed computing on larger-than-memory dataset
  - **Metadata Server**: full DuckDB SQL support to query your embedded metadata
  - **On-the-fly Build**: keep your data in original format (.zvi, ndtiff etc). No staging or on-boarding process needed
  - **Built-in Viewer**: browse all your data with any browser (e.g., on an ipad)

### Quick Start
```sh
curl -fsSL https://biopb.org/install.sh | bash
biopb server start
```
Point your browser to the url printed in log

## Biopb-Image

Deploy complex image processing algorithms (e.g., large deep-learning models) on the network as services, including pre-built containers for popular algorithms (e.g., segmentation). [Read More...](https://github.com/biopb/biopb-server)

## Napari-Biopb

GUI app for the end-users. The power of biopb in a familiar interface. [Read More...](https://github.com/biopb/napari-biopb)

## SDK

Schema, utilities and cli for building your own workflow. Explore your data in jupyter notebook etc.

#### Python

```sh
pip install biopb[tensor]
```

#### Java

```xml
<dependency>
  <groupId>io.github.jiyuuchc</groupId>
  <artifactId>biopb</artifactId>
  <version>CURRENT_VERSION</version>
</dependency>
```
