v1.0.0

README.md

@@ -2,7 +2,7 @@
 
 <div align="center">
 
-[![HistoJS logo](https://github.com/Mmasoud1/HistoJS/blob/main/Demo/histoJS.png)]()
+[![HistoJS logo](https://lh3.googleusercontent.com/Q3eYJfpQMety3sUUTLKeZKLkJBzx-NmLZNn1NphdWs9hBNYmfHCzZTphddpXDcfUxjtaHTXTr89R57LieZflqUsGHM3TxtIbVNoQOKf3ZbPjB01C8gYANmezAzq4JgUU=w1823)]()
 
  [![Github contributors](https://img.shields.io/badge/contributors-*-brightgreen)](https://github.com/Mmasoud1/HistoJS/graphs/contributors) [![licence ](https://img.shields.io/badge/license-BY--NC--ND-orange)](https://creativecommons.org/licenses/by-nc-nd/3.0/) [![Python ](https://img.shields.io/badge/python-3.5%20%7C%203.6%20%7C%203.7-blue)]()[![JS ](https://img.shields.io/badge/Types-JavaScript-blue)]()
 [![HW ](https://img.shields.io/badge/HardWare-GPU-green)]()
@@ -12,9 +12,9 @@
 
 
 
-HistoJS is an interactive tool to manage, manipulate, store and analysis the multi-channels OME-Tiff files .
+HistoJS is an interactive tool to manage, store and analysis the multi-channels OME-Tiff files.
 
-The tool is using [Digital Slide Archive (DSA)](https://styx.neurology.emory.edu/girder/#) as a backbone to host OME files and update the image metadata remotely or locally. 
+The tool is using Digital Slide Archive as a backbone to update the image metadata remotely or locally.
 
 - Install requirements
 ```bash
@@ -34,7 +34,6 @@ After creating the histojs environment, from the root level of the repository op
     source activate histojs
     python RestApi.py
 ```
-A dockerized version for the RestApi will be released soon. 
 
 To run the localhost in the browser, just start up a simple local server from the root level of the repository with any available port number 8xxx (e.g. 8020)
 
@@ -51,25 +50,18 @@ To run the localhost in the browser, just start up a simple local server from th
       
 
 
-## Dataset
+A dockerized version will be released soon for the api. 
 
-OME-Tiff  and their channels metadata CSV files must be hosted on a DSA server. To host your dataset you need to create a user account on any DSA servers such as [Styx](https://styx.neurology.emory.edu/girder/#) and upload your OME image, cells mask(optional), and channels metadata CSV file to your collection as in this [example](https://styx.neurology.emory.edu/girder/#folder/5e361c5c34679044bda81b11):
+For using the backbone DSA server, you need to create a user account on any DSA servers and upload your OME image, cells mask, and channels metadata CSV file to your collection as in this link:
 
 ```bash
     https://styx.neurology.emory.edu/girder/#folder/5e361c5c34679044bda81b11
 ``` 
 
-If you need to install DSA server locally on you machine and host your data locally please follow this [link](https://github.com/DigitalSlideArchive/digital_slide_archive/tree/master/ansible).
 
+Please note: if the name of the OME image file is $fileName$.ome.tif (e.g. TONSIL-1_40X.ome.tif), the cell mask must be $fileName$_cellMask.tiff (e.g. TONSIL-1_40X_cellMask.tiff), and the Channel metadata CSV file should be $fileName$_channel_metadata.csv (e.g. TONSIL-1_40X_channel_metadata.csv)
 
-### File naming conventions: 
-
-```bash
-- The OME image file must be $fileName$.ome.tif (e.g. TONSIL-1_40X.ome.tif).
-- The cell mask if available must be $fileName$_cellMask.tiff (e.g. TONSIL-1_40X_cellMask.tiff).
-- The Channel metadata CSV file should be $fileName$_channel_metadata.csv (e.g. TONSIL-1_40X_channel_metadata.csv).
-- The Channel metadata CSV file must have at least two columns: 'channel_number' and 'channel_name'.
-```
+The Channel metadata CSV file must have at least two columns: 'channel_number' and 'channel_name'
 
 
 
@@ -94,4 +86,3 @@ For creating OME channel groups, browse to your server file and click design mod
 **Copyright 2021 Mohamed Masoud**
 </div>
 
-