Merge pull request #175 from IPMI-ICNS-UKE/Dejan_local

docs repair

README.md

@@ -1,4 +1,65 @@
-# C-DARTS
-A Ca2+ microdomain analysis pipeline for spatio-temporal microscopy imaging of T cells
+# DARTS
 
+![overview](/docs/assets/img/Figure_1_dart.png)
+
+## About
+**DARTS** is an integrated tool for the analysis of Ca<sup>2+</sup> microdomains in immune cells (Jurkat T cells, primary murine cells, NK).
+For detailed information, see the [Documentation](https://ipmi-icns-uke.github.io/DARTS/).
+
+It combines the following modules:
+
+- Postprocessing
+   - channel registration
+   - background subtraction
+   - cell detection and tracking
+   - deconvolution
+   - bleaching correction
+   - ratio computation 
+- Shape Normalization
+- Hotspot Detection and Dartboard visualization (based on [2])
+
+
+
+## Installation 
+We recommend using [anaconda](https://www.anaconda.com/download) to install the necessary packages.
+
+Download and install anaconda and python and either clone the DARTS code with 
+``
+git clone https://github.com/IPMI-ICNS-UKE/DARTS.git
+``
+
+or download the .zip file via the download button. Before continuing, please check the prerequisites on the Installation page in the [Documentation](https://ipmi-icns-uke.github.io/DARTS/General/Installation.html).
+
+Navigate to the folder containing the `DARTS.yml` file and run 
+
+```
+conda env create -f DARTS.yml
+conda activate DARTS
+```
+
+in the command line. 
+
+For more information regarding the installation, see the [Documentation](https://ipmi-icns-uke.github.io/DARTS/)
+
+
+## Usage
+1. Store raw image files in a source directory. All common microscopy image formats can be opened, e.g. ics- or tif-files. 
+2. Run `python main.py` in the terminal/ shell/ powershell or IDE of your choice.
+3. Enter relevant information in the GUI. 
+4. If necessary, define the bead contacts for each cell of interest in each image file.
+
+![Main](https://github.com/IPMI-ICNS-UKE/DARTS/assets/127941319/3549d0d5-5f8d-4d47-bf8c-096202c99bb0)
+![Bead contacts](https://github.com/IPMI-ICNS-UKE/DARTS/assets/127941319/d145d44f-f154-4125-b15d-3b82a40c788a)
+
+
+
+## License
+This code runs under the Apache 2.0 license.
+
+## References and Citing
+If DARTS is useful for a project that leads to publication, please acknowledge DARTS by citing it.
+
+[1]  DARTS: an open-source Python pipeline for Ca2+ microdomain analysis in live cell imaging data 
+
+[2] Diercks BP, Werner R, Schetelig D, Wolf IMA, Guse AH. High-Resolution Calcium Imaging Method for Local Calcium Signaling. Methods Mol Biol. 2019;1929:27-39. doi: [https://doi.org/10.1007/978-1-4939-9030-6_3](https://doi.org/10.1007/978-1-4939-9030-6_3)