Nanoscopy Python library (NanoPyx, the successor to NanoJ) - focused on light microscopy and super-resolution imaging
---

#### What is the NanoPyx 🔬 Library? #### 

NanoPyx is a library specialized in the analysis of light microscopy and super-resolution data.
It is a successor to NanoJ, which is a Java library for the analysis of super-resolution microscopy data.

NanoPyx focuses on performance, by heavily exploiting cython aided multiprocessing and simplicity. It implements methods for the bioimage analysis field, with a special emphasis on those developed by the Henriques Laboratory.

---

#### Short Video Tutorials #### 

| What is NanoPyx? | 
https://youtu.be/iAdgusBAU0Q
| How to use NanoPyx in Google Colab? |
https://youtu.be/KD0RzolFnd4

---

#### napari plugin #### 

NanoPyx is also available as a napari plugin, which can be installed via pip:

```pip install napari-nanopyx```

---

#### Installation #### 

`NanoPyx` is compatible and tested with Python 3.9, 3.10, 3.11 in MacOS, Windows and Linux. Installation time depends on your hardware and internet connection, but should take around 5 minutes.

You can install `NanoPyx` via [pip]:

```pip install nanopyx```

If you want to install with support for Jupyter notebooks:

```pip install nanopyx[jupyter]```

or if you want to install with all optional dependencies:

```pip install nanopyx[all]```

To install latest development version:

```pip install git+https://github.com/HenriquesLab/NanoPyx.git```

To install directly from source code, alongside all dependencies, navigate to the source folder:

```pip install -e .[all]

NOTES FOR MAC USERS

If you wish to compile the NanoPyx library from source, you will need to install the following dependencies:

- Homebrew from https://brew.sh
- gcc, llvm and libomp from Homebrew through the command:

```brew install gcc llvm libomp```

---

#### Usage #### 

Depending on your preferences and coding proficiency you might be using NanoPyx differently. 

- If you are using Jupyter Notebooks or Google Colab notebooks check out our (https://youtu.be/KD0RzolFnd4)
- If you are using our napari plugin check out the official napari tutorial and stay tuned for more
- If you prefer to use the Python library and take full advantage of the Liquid Engine flexibility, check out our Liquid Engine templates and our official documentation (https://henriqueslab.github.io/NanoPyx/nanopyx.html).

---

#### License #### 

Distributed under the terms of the [CC-By v4.0] license,
"NanoPyx" is free and open source software

---
