GUI

README.rst

@@ -1,7 +1,7 @@
 Stitching
 =========
 
-Stitch images to form a montage.
+Stitch images to form a montage. A montage contains of a n-by-n grid, where in each grid compartment an image can be placed, e.g., a 5-by-5 montage contains 25 images in total. Visit http://cellprofiler.org/imagingflowcytometry/ for more information on the imaging flow cytometry workflow and the image stitching (also referred to as image tiling).
 
 Requirements
 ============
@@ -24,6 +24,9 @@ click
 skimage
   $ pip install skimage
 
+Tkinter
+  typically included with your python distribution
+
 python-bioformats
   $ pip install python-bioformats
 
@@ -43,11 +46,19 @@ Installation
 
 Use
 ===
+Generates per-channel montages from IMAGE saved to OUTPUT_DIRECTORY. Each image in IMAGE has shape 55px by 55px and is padded with random noise. Montage files are named "ch1.tif", "ch2.tif", ..., one for each channel.
+
+Open a new command line window (also called command prompt window in Windows OS or terminal in MAC OS). Now, to generate the montages, you can either (1) start the stitching GUI or (2) use the command line.
+
+1. To use the GUI, type
+  $ python stitching
+The GUI window will open where you can select a .cif file to generate the montages. Optionally you can also display selected images from the .cif file.
+
+OR
 
-  $ python stitching -o path/to/OUTPUT_DIRECTORY path/to/IMAGE
+2. To use the command line, type
+  $ python stitching -image='path/to/IMAGE' -output='path/to/OUTPUT_DIRECTORY'
 
-Generates per-channel tiled images from IMAGE saved to OUTPUT_DIRECTORY. Each image in IMAGE has shape 55px by 55px and
-is padded with random noise. Files are named "ch1.tif", "ch2.tif", ..., one for each channel.
 
 Optional: