diff --git a/README.md b/README.md index 1a8d937..2af858d 100644 --- a/README.md +++ b/README.md @@ -1,21 +1,10 @@ -# Synaptic Reconstruction +# SynapseNet: Deep Learning for Automatic Synapse Reconstruction -Reconstruction of synaptic structures in electron microscopy. +SynapseNet is a tool for segmentation and analysis of synapses in electron microscopy. -THIS IS WORK IN PROGRESS! +To learn how to use SynapseNet, check out [the documentation](https://computational-cell-analytics.github.io/synapse-net/). +To learn more about how it works, check out [our preprint](TODO). -## Installation - -- Make sure conda or mamba is installed. - - If you don't have a conda installation yet we recommend [micromamba](https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html) -- Create the environment with all required dependencies: `mamba env create -f environment.yaml` -- Activate the environment: `mamba activate synaptic-reconstruction` -- Install the package: `pip install -e .` - -## Tools - -### Segmentation Correction - -https://napari.org/stable/howtos/layers/labels.html - -### Distance Measurements +See an example reconstruction of a mossy fibre synapse with SynapseNet. +Automatic segmentation of synaptic vesicles are rendered in orange, active zones in blue and two mitochondria in red and cyan. +![Reconstruction of a mossy fiber synapse](doc/images/synapse-reconstruction.png) diff --git a/doc/images/synapse-reconstruction.png b/doc/images/synapse-reconstruction.png new file mode 100644 index 0000000..b7cf058 Binary files /dev/null and b/doc/images/synapse-reconstruction.png differ diff --git a/doc/start_page.md b/doc/start_page.md index b70582d..3b26844 100644 --- a/doc/start_page.md +++ b/doc/start_page.md @@ -14,15 +14,25 @@ especially throught the [domain adaptation](domain-adaptation) functionality. SynapseNet offers a [napari plugin](napari-plugin), [command line interface](command-line-interface), and [python library](python-library). Please cite our [bioRxiv preprint](TODO) if you use it in your research. -## Installation +**The rest of the documentation will be updated in the next days!** + +## Requirements & Installation - Requirements: Tested on Linux but should work on Mac/Windows. - GPU needed to use 3d segmentation networks - Installation via conda and local pip install - GPU support +- Make sure conda or mamba is installed. + - If you don't have a conda installation yet we recommend [micromamba](https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html) +- Create the environment with all required dependencies: `mamba env create -f environment.yaml` +- Activate the environment: `mamba activate synaptic-reconstruction` +- Install the package: `pip install -e .` + ## Napari Plugin +lorem ipsum + ## Command Line Functionality - segmentation cli