1_Z_project_and_contrast_imageJ_macro.ijm : From the raw .tiff files, average the slices and tweak intensity and contrast. Outputs the flattened image as a .tiff in a dedicated subfolder "Z_proj" in the same directory as the input files. Doesn't process stacks containing the wrong number of slices (filters out faulty recordings).
2_Alignment_and_drift_imageJ_macro.ijm : This script select the correct files for alignment according to user input ( All zeros, X displacement, Y displacement or ALL) It assumes that each direction (x, -x, y, -y) has 2 repeats, and that only the relevant files are in the input folder. i.e. user needs to place all the incorrect files (non filtered out by the previous macro) in a different folder or subfolder for it to work it then uses the the "Linear Stack Alignment with SIFT" plugin to align tiles. Exports translation values as a .csv file for each subset of data, and a tile image showing the displacement :
1_Z_project_and_contrast_imageJ_macro.ijm : From the raw .tiff files, average the slices and tweak intensity and contrast. Outputs the flattened image as a .tiff in a dedicated subfolder "Z_proj" in the same directory as the input files. Doesn't process stacks containing the wrong number of slices (filters out faulty recordings).
2_Alignment_and_drift_imageJ_macro.ijm : This script select the correct files for alignment according to user input ( All zeros, X displacement, Y displacement or ALL) It assumes that each direction (x, -x, y, -y) has 2 repeats, and that only the relevant files are in the input folder. i.e. user needs to place all the incorrect files (non filtered out by the previous macro) in a different folder or subfolder for it to work it then uses the the "Linear Stack Alignment with SIFT" plugin to align tiles. Exports translation values as a .csv file for each subset of data, and a tile image showing the displacement :
Zero_only_translation.csv