SliceNicer

SliceNicer is an ImageJ macro for normalization of time lapse images against a reference image

Content

• Content
• Screenshot
• Usage
• Getting started
  • Notes
  • Download
  • Installation via fiji-installer.bat (windows only)
  • Manual installation

Screenshot

Usage

1. Import .lsm file (containing the timelapse) into ImageJ
2. Choose a line ROI which represents the image (e.g. 1000px length and 1000px width) and save it via the ROI manager as .roi file
3. Note which image should be used as reference for normalisation Close all windows except the main ImageJ window.
4. You should now have two files
   • the .lsm file
   • the .roi file
5. Open the macro via Plugins > SliceNicer_v#.#.#
6. Adjust settings:
   • Username: the username of the user who is logged on to the computer
   • Input file: the present .lsm file
   • ROI file: the present .roi file
   • Output directory: the directory where the export folder containing all output files will be created (if the default directory is chosen, the folder content will be overwritten with each application)
   • Reference image: the number of the previously noted reference image (for the first image: 1)
   • Load stack after processing: Keeping this checked is recommended, this will:
     • load all normalized images as hyperstack
     • save the hyperstack as .tiff file
     • create timelapse videos of all channels of the hyperstack

Getting started

Notes

• The input file must be in .tiff format or any other TIFF dependent format (e.g. .lsm)
• The fiji-installer only works with Fiji, not with plain ImageJ

Download

SliceNicer_v1.2.5.zip - September 7, 2022 - 3.45 KB

Installation via fiji-installer.bat (windows only)

1. Download the latest macro version using the download link (see above)
2. Extract the .zip file
3. Run the fiji-installer.bat to copy the file to the correct location and delete deprecated versions
4. Restart ImageJ
5. The macro can now be found under Plugins (at the bottom of the dropdown menu)

Manual installation

1. Download the latest macro version using the download link (see above)
2. Extract the .zip file
3. Open ImageJ or Fiji
4. Go to Plugins > Install... and select the extracted SliceNicer_#.#.#.ijm file.
5. Restart ImageJ
6. The macro can now be found under Plugins (at the bottom of the dropdown menu)