SSAM-lite is a lightweight, browser-based implementation of the SSAM framework. It provides the functionality of SSAMs most popular and widely used features in a graphical user interface -with a few functions added for convenience and ease of use.
-TODO what does SSAM do
+with a few functions added for convenience and ease of use. It neiteher requires specialised computational experts +nor hardware to handle and process data and thus can be run on a modest laptop. +The SSAM framework allows for cell segmentation-free identification of cell-types by integrating prior knowledge of +cell type-specific gene signatures with data from a variety of spatial in situ transcriptomics techniques.
TODO please correct me!
@@ -118,7 +119,6 @@TODO -We should add some stuff about requirments etc
+We should add some stuff about requirements etcconda install flask numpy pandas
cd /ssamLiteDev/scripts/flask -export FLASK_APP=run.py -export FLASK_ENV=development -flask run
-Open browser at 127.0.0.1:5000
+And start the server.
+cd /ssamLiteDev/scripts/flask
+export FLASK_APP=run.py
+export FLASK_ENV=development
+flask run
+Type in the address bar of your browser: 127.0.0.1:5000
This definitely needs to be explained. However, somebody with a little bit expertise should do this, most of it will be config dependent and people installing this will most likely know what they are doing!
@@ -139,7 +138,7 @@TODO do we need a tutorial? there is not a lot of room between the quickstart and the usage anyway?
-After installation of SSAM-lite, this tutorial will help you get to -know the basic workflow of
-SSAM-lite-solo runs locally on your computer. It is executed by your Browser -and to open it you onyl need to navigate to the unzipped SSAM-lite directory -and double-click the index.html to open it in your default Web Browser.
+SSAM-lite-solo runs locally on your computer. It is executed by your browser +and to open it you only need to navigate to the unzipped SSAM-lite directory +and double-click the index.html and it will start in your default web browser.
To connect to SSAM-lite-server, you will need to to open your favourite Web Browser (not IE) -and enter the correct IP address and port in the form {ip}:{port} (e.g. 127.0.0.1:5000). +
To connect to SSAM-lite-server, you will need to to open your favourite web browser (not IE) +and type the correct IP address and port in the form {ip}:{port} (e.g. 127.0.0.1:5000) into the address bar. However, the IP and port depends on your local setup. Talk to your responsible SSAM-lite coordinator.
The Data will be uploaded in the Data Center section of the tool. By clicking the “Coordinates” +
The data will be uploaded in the Data Center section of the tool. By clicking the “Coordinates” or “Signatures” button and selecting the correct files. To be able to use SSAM-lite you need to prepare your data in csv format. Two input files are required and must be structured as follows:
This file needs to be of the form Gene, x-coordinate, y-coordinate. +
This file needs to be of the form gene, x-coordinate, y-coordinate. The name of the headers are irrelevant, however their order needs to be kept. Negative coordinates are possible and the units do not matter. However, their magnitude might have an influence on proper parameter values later on.
@@ -127,30 +126,30 @@Gene
x
gene,
x,
y
Gene A
0.5
gene A,
0.5,
1.3
Gene A
1.1
gene A,
1.1,
2.1
Gene B
0.4
gene B,
0.4,
0.5
This file should be a matrix of Cell types by Genes. -The first column and row contains the names of Cell types and Genes, respectively. All the other cell values +
This file should be a matrix of cell types by genes. +The first column and row contains the names of cell types and genes, respectively. All the other cell values are gene scores … TODO how to define this … This will later be used to assign each pixel to a cell type (or leave them unclassified) -based on the Kernel Density Estimation.
+based on the kernel density estimation.
