Merge pull request #46 from HiDiHlabs/dev

Release 1
HiDiHlabs · Oct 2, 2021 · 011280c · 011280c
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diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 # SSAM-lite
 
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](./LICENSE)
-[![DOI:10.1101/2021.09.2x.xxxxxxxx](http://img.shields.io/badge/DOI-10.1101/2021.09.2x.xxxxxxxx-B31B1B.svg)](https://doi.org/10.1101/2021.09.2x.xxxxxxxx)
+[![DOI:10.1101/2021.09.29.462194](http://img.shields.io/badge/DOI-10.1101/2021.09.29.462194-B31B1B.svg)](https://doi.org/10.1101/2021.09.29.462194)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5517607.svg)](https://doi.org/10.5281/zenodo.5517607)
 [![Netlify Status](https://api.netlify.com/api/v1/badges/eba53f5b-8273-4ac3-9d7b-fcb577e2815c/deploy-status)](https://app.netlify.com/sites/ssam-lite/deploys)
 
@@ -37,17 +37,16 @@ https://ssam-lite.readthedocs.io
 
 This project follows the [SemVer](https://semver.org) guidelines for versioning.
 
-For a list of versions see the [releases](https://github.com/HiDiHlabs/ssam-lite/releases).
+For a list of versions see the [releases](https://github.com/HiDiHlabs/ssam-lite/releases)
+and the [release notes](./ReleaseNotes.txt).
 
 
 ## Citations
 
-TODO update Citation when ready
-
-Sebastian Tiesmeyer, Shashwat Sahay, Niklas Mueller-Boetticher, Roland Eils, Sebastian Mackowiak, Naveed Ishaque.
+Sebastian Tiesmeyer, Shashwat Sahay, Niklas Müller-Bötticher, Roland Eils, Sebastian D. Mackowiak, Naveed Ishaque.
 2021.
-"[SSAM-lite: a light-weight web-based framework for analysis of spatially resolved transcriptomics data](https://biorxiv.org)"
-*bioRxiv*. doi: 10.1101/2021....
+"[SSAM-lite: a light-weight web app for rapid analysis of spatially resolved transcriptomics data](https://www.biorxiv.org/content/10.1101/2021.09.29.462194)"
+*bioRxiv*. doi: 10.1101/2021.09.29.462194
 
 
 ## Sample data

diff --git a/ReleaseNotes.txt b/ReleaseNotes.txt
@@ -1,5 +1,8 @@
+1.0.0
+- First release
+
 0.2.1
--Bugfix for version display and drag-and-drop
+- Bugfix for version display and drag-and-drop
 
 0.2.0
 - Version and copyright added to interface

diff --git a/docs/res/imgs/ControlPanel.png b/docs/res/imgs/ControlPanel.png
diff --git a/docs/res/imgs/DownloadPlot.png b/docs/res/imgs/DownloadPlot.png
diff --git a/docs/res/imgs/KDE.png b/docs/res/imgs/KDE.png
diff --git a/docs/res/imgs/KDE_Optimization.png b/docs/res/imgs/KDE_Optimization.png
diff --git a/docs/res/imgs/ParameterPreview.png b/docs/res/imgs/ParameterPreview.png
diff --git a/docs/res/imgs/Threshold_Optimization.png b/docs/res/imgs/Threshold_Optimization.png
diff --git a/docs/res/imgs/inferredCelltypes.png b/docs/res/imgs/inferredCelltypes.png
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -22,7 +22,7 @@
 author = 'Niklas Müller-Bötticher'
 
 # The full version, including alpha/beta/rc tags
-release = '0.1'
+# release = '0.1'
 
 
 # -- General configuration ---------------------------------------------------

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -17,12 +17,11 @@ cell type-specific gene signatures with data from a variety of spatial in situ t
 Citations
 =================
 
-TODO please correct me!
-
-Sebastian Tiesmeyer, Shashwat Sahay, Niklas Mueller-Boetticher, Roland Eils, Sebastian Mackowiak, Naveed Ishaque.
+Sebastian Tiesmeyer, Shashwat Sahay, Niklas Müller-Bötticher, Roland Eils, Sebastian D. Mackowiak, Naveed Ishaque.
 2021.
-"`SSAM-lite: a light-weight web-based framework for analysis of spatially resolved transcriptomics data <https://biorxiv.org>`__"
-*bioRxiv*. doi: 10.1101/2021....
+"`SSAM-lite: a light-weight web app for rapid analysis of spatially resolved transcriptomics data <https://www.biorxiv.org/content/10.1101/2021.09.29.462194>`__"
+*bioRxiv*. doi: 10.1101/2021.09.29.462194
+
 
 
 .. toctree::

diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -19,7 +19,7 @@ Requirements
 ============
 
 SSAM-lite and SSAM-lite-server should run on all modern browsers supporting JavaScript
-and webGL. It has been verified to run on Firefox, Chrome, Edge and Safari.
+and WebGL. It has been verified to run on Firefox, Chrome, Edge and Safari.
 
 SSAM-lite requires an internet connection to access the TensorFlow.js (v2.0.0) 
 library.
@@ -36,7 +36,7 @@ SSAM-lite
 
 SSAM-lite is accesible via https://ssam-lite.netlify.app, and does not need to be installed.
 
-However, if you want to have a local copy of the code, installation is possible and 
+However, if you want to have a local copy of the code or run an older version, installation is possible and 
 could not be easier. You either clone the `GitHub repository <https://github.com/HiDiHlabs/ssam-lite>`__
 
 .. code-block:: bash

diff --git a/docs/source/quickstart.rst b/docs/source/quickstart.rst
@@ -33,8 +33,8 @@ Click on "Get going!"
 You are in the **Data Center** now. Click on "Coordinates" and select the *coordinates.csv* from the *Codeluppi_osmFISH* directory in the test data.
 Do the same for the "Signatures" (obviously use the *signature.csv* from the same directory this time, *duh!*)
 
-In the **Parameters** section leave the *Vector field wdith* at its default, set the *KDE kernel bandwidth* to 5 and the 
-*Cell assignment threshold* to 50.
+In the **Parameters** section leave the *pixel wdith* at its default, set the *KDE kernel bandwidth* to 5 and the 
+*expression threshold* to 50.
 
 The time is flying by so we head straight for **Analysis** without any further explanation and click on 
 "Run Kernel Density Estimation". Time for a short break now, this step might take a few seconds.

diff --git a/docs/source/usage.rst b/docs/source/usage.rst
@@ -15,11 +15,10 @@ Test Data
 If you want to follow our usage guide along with some sample data you can download a sample data set from
 Zenodo (https://zenodo.org/record/5517607).
 
-Three sample data sets are available:
+Two sample data sets are available:
 
 #. **Codeluppi_osmFISH**: an osmFISH dataset of the mouse somatosensory cortex from `Codeluppi et al., Nature methods, 2018 <https://www.nature.com/articles/s41592-018-0175-z>`__.
 #. **Tosti_ISS_Pancreas**: an ISS dataset of the human pancreas from `Tosti et al., Gastroenterology, 2021 <https://doi.org/10.1053/j.gastro.2020.11.010>`__.
-#. **Qian_ISS_CA1**: ISS datasets of the mouse hippocampal area CA1 from `Qian et al., Nature methods, 2020 <https://www.nature.com/articles/s41592-019-0631-4>`__.
 
 The datasets have been modified to fit the SSAM-lite input format. You can also find further information on the datasets
 (such as number of mRNA spots etc.) on Zenodo or the *README* file within each directory once you downloaded it.
@@ -76,8 +75,8 @@ SSAM-lite lets you interactively explore and adjust the plots to your needs.
 Alternatively, when hovering over a plot a small control panel will be displayed in the top right corner
 which offers some additional functionality.
 
-.. image:: ../res/imgs/Control Panel.png
-        :width: 300
+.. image:: ../res/imgs/ControlPanel.png
+        :width: 250
         :align: center
         :alt: Control panel for plots    
 
@@ -157,16 +156,16 @@ however we will briefly describe the purpose and effect of the parameters
 that can be set by the user to obtain optimal results.
 
 
-Vector field width
-    The vector field width defines the horizontal pixel count of the output images.
+Pixel width
+    The pixel width defines the horizontal pixel count of the cell type map.
     This is necessary as the kernel density estimation (KDE) will be projected onto 
     discrete locations (the pixels).
 
-    A higher value will result in higher resolution but also in increased processing time and memory
-    as well as size of the output images.
+    A higher value will result in higher resolution but also in increased processing 
+    time and memory.
 
 
-KDE kernel bandwidth (sigma)
+KDE kernel bandwidth
     SSAM-lite uses a Gaussian kernel and the kernel bandwidth defines the "range" of 
     integration of data points (mRNA spots) for the KDE.
 
@@ -178,7 +177,7 @@ KDE kernel bandwidth (sigma)
         :alt: Screenshot of two different kernel bandwidth
 
 
-Cell assignment threshold
+Expression threshold
     This threshold is used to decide whether a pixel in the KDE projection belongs to
     a cell or not. 
 
@@ -187,25 +186,26 @@ Cell assignment threshold
 
     .. image:: ../res/imgs/Threshold_Optimization.png
         :width: 650
-        :alt: Screenshot of two cell assignment thresholds
+        :alt: Screenshot of two expression thresholds
 
 Parameter preview and adjustment
 --------------------------------
 
-Each of the parameters can be set in their respective field and applied by hitting *Enter*.
-For a more intuitive parameter selection you can open a preview by clicking "Use preview generator for parameter search".
+Each of the parameters can be set in their respective field. For a more intuitive parameter selection you can open a preview 
+by clicking "Use preview generator for parameter search".
 This will display the results of a subset of your data with the currently set parameters and lets you 
 interactively explore and tune your parameter set. To adjust the preview area click into the left-most plot and wait for
-the browser to recalculate (this might take a few moments).
+the browser to recalculate (this might take a few moments). When the "Live update" functionality is enabled the plots will 
+be updated automatically if you change any of the parameters.
 
 .. image:: ../res/imgs/ParameterPreview.png
   :width: 800
   :alt: Screenshot of the Parameter preview section
 
 Once you are happy with your choice you can proceed with the actual analysis.
 
-For our example analysis we are going to proceed with a *Vector field width* of 1500, a *KDE kernel bandwidth*
-of 3, and a *Cell assignment threshold* of 12.
+For our example analysis we are going to proceed with a *pixel width* of 1500, a *KDE kernel bandwidth*
+of 2.5, and an *expression threshold* of 13.
 
 
 Analysis