This is the homepage for the code for the Methods Paper "Immunofluorescence detection and quantification of phosphorylated SMAD protein expression in human blastocysts" by Todd Fallesen and Sophie Brumm.
There are files for FIJI, CellProfiler and Matlab
The Fiji files are used in image preprocessing. split_channels_multiple_series_and_rename.ijm: This code is used to prepare the images for use in CellProfiler. Images are split into individual channels and Z-frames using this script. The number of exported images will be equal to the number of channels multiplied by the number of Z-slices in the original image. The script will work on images with multiple series, such as LIF files. Stardist_process_folder.ijm This code will run a StarDist segmentation on every image of a specified channel. The output of this script is a StarDist label image for each input image. Enhance_All_C2_C3_c4.ijm This is an optional script for background subtraction and contrast enhancement of images to aid in image processing.
There are two cellprofiler project files. SHRUMS_4_Channels_Enhanced__Channels_For_Star_Methods.cpproj Set up to run on a 4 channel image SHRUMS_5_Channels_Enhanced__Channels_For_Star_Methods.cpproj Set up to run on a 5 channel image
SHRUMS_Wrangling_4_channels.m Performs the data wrangling of the output from the 4 channel cellprofiler pipeline in Matlab SHRUMS_Wrangling_5_channels.m Performs the data wrangling of the output from the 5 channel cellprofiler pipeline in Matlab
SHRUMS_Wrangling_4_channels.ipynb Performs the data wrangling of the output from the 4 channel cellprofiler pipeline in python SHRUMS_Wrangling_5_channels.ipynb Performs the data wrangling of the output from the 5 channel cellprofiler pipeline in python