ALIBY: End-to-end processing for high throughput microscopy
This framework orchestrates a multitude of different tools to process imaging data.
NOTE: This past year ALIBY went through heavy refactoring. The documentation is under (re)construction.
By modality:
- Time series microscopy
- Fluorescence microscopy (e.g., Cell Painting)
By procedure
- Segmentation (e.g., Cellpose) + Feature (e.g., cp_measure, engineered features)
- Deep Learning models (e.g., DinoV3, OpenPhenom)
By backend
- Within the same environment (Cellpose -> cp_measure)
- Communicating with other environments (via Nahual)
Installation
We recommend using uv to install aliby
Once uv is installed, we suggest running
git clone git@github.com:afermg/aliby.git
cd aliby
uv sync --all-extras
Nix installation
For reproducible environments using Nix flakes and envrc.
To run a self-contained virtual environment shell session
nix develop .
For convenience, to start the environment every time you access the project you automatically set the environment
direnv allow .
Release files for aliby 0.2.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| aliby-0.2.1.tar.gz | 98.1 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| aliby-0.2.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 218.6 kB
Release files / aliby-0.2.1.tar.gz
| Download URL | aliby-0.2.1.tar.gz |
|---|---|
| Size | 98.1 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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|
|
BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
uv/0.6.10
|
Release files / aliby-0.2.1-py3-none-any.whl
| Download URL | aliby-0.2.1-py3-none-any.whl |
|---|---|
| Size | 120.5 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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|
|
BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
uv/0.6.10
|
