diff --git a/README.md b/README.md index 580d38b..81da551 100644 --- a/README.md +++ b/README.md @@ -19,13 +19,19 @@ Zarrcade is a web application for easily browsing, searching, and visualizing co ## Getting Started - ### 1. Install miniforge [Install miniforge](https://docs.conda.io/en/latest/miniforge.html) if you don't already have it. -### 2. Initialize the conda environment +### 2. Clone this repo + +```bash +git clone https://github.com/JaneliaSciComp/zarrcade.git +cd zarrcade +``` + +### 3. Initialize the conda environment ```bash conda env create -f environment.yml @@ -38,7 +44,7 @@ conda activate zarrcade See the [Example](#example) section below to try out the example before working with your own data. -### 3. Create OME-Zarr images +### 4. Create OME-Zarr images If your images are not already in OME-Zarr format, you will need to convert them, e.g. using bioformats2raw: @@ -49,7 +55,7 @@ bioformats2raw -w 128 -h 128 -z 64 --compression zlib /path/to/input /path/to/za If you have many images to convert, we recommend using the [nf-omezarr Nextflow pipeline](https://github.com/JaneliaSciComp/nf-omezarr) to efficiently run bioformats2raw on a collection of images. This pipeline also lets you scale the conversion processes to your available compute resources (cluster, cloud, etc). -### 4. Import images and metadata into Zarrcade +### 5. Import images and metadata into Zarrcade You can import images into Zarrcade using the provided command line script: @@ -76,7 +82,7 @@ relative/path/to/ome2.zarr,JDH3562,Blu Read more about the import options in the [Data Import](./docs/DataImport.md) section of the documentation. -### 5. Run the Zarrcade web application +### 6. Run the Zarrcade web application Start the development server, pointing it to your OME-Zarr data: