Utilities ImageJ Macros and other scripts by MICC Cell Observatory team

Content

ScaleAndCropImages: Utility program to help scaling, cropping and saving (as tiff or hdf5) multiple EM images in preparation for further analysis

ExportImagesFromComplexMicroscopyFiles: Export individual images From Complex Microscopy file (lif, czi, nd2) to Tiff or hdf5 Files

RunIlastikHeadless.bat: Windows bat file for running Ilastik Pixel Classifier followed by Ilastik boundary based segmentation on all files in a given folder.

Written by: Ofra Golani at the MICC Cell Observatory, Weizmann Institute of Science

Software package: Fiji (ImageJ)

Workflow language: ImageJ macro

ScaleAndCropImages

Overview

Utility program to help scaling, cropping and saving multiple EM images in preparation for further analysis Go over all images (see details below), for each image:

• Open the image
• prompt the user to draw a line along the scalebar
• prompt the user to select region-of-interest to keep , usually you will select the whole area without the scalebar and the rest of the EM microscope information

Control Options

• ResultsLocation: Two options for saving results:
• UnderOrigFolder: save under InputFolder/Scaled OR
• InNewLocation: resScaledFolder/FolderName
• OutputFileType: allow saving cropped file into either tif or ilastik hdf5 format (for further training ilastik classifier suitable for running from Fiji)

The following strategies are employed to allow fast scaling and cropping:

• let you process single image OR whole folder of images OR all images in all subfolders of a selected folder
• let you select subset of images that macth specific folder and file names pattern (FolderNamePattern, FileNamePattern)
• use default ScaleBar (controlled by DefaultKnownDist)
• use the by default same scalebar ROI and same cropping region as used for the previous image , and let you change them if needed
• save scaled image and cropping region in a file under "ScaledImages" subfolder, this enables processing only of images that were not processed before OR repeated cropping without rescaling, OR correction for few images
• final output (scaled and cropped) images are saved in different location under "ScaledAndCroppedImages" subfolder"

ExportImagesFromComplexMicroscopyFiles

Overview

Export individual images From Complex Microscopy file (lif, czi, nd2) to Tiff Files

Input: Single complex file named eg XX.lif or folder of complex files Output: for each lif file: Subfolder named XX_Tif with the individual series saved as tif files

Control Options

• Controled by a dialog box
• Export all Images / Export Last series / Export the N series / Export only images that match criteria on size/number of channels
• Match Criteria:
  • number of channels
  • image size
  • image name include specified Text
  • Processing Type: None/MaxProject/Extract single channel
• Output type: Tif / hdf5 / ilastik hdf5 / jpg / png
• Location of output files: UnderOrigFolder / InNewLocation this option usefull especially for working with files stored on network disks such as BioImg storage server (for WIS users)
• Exported image files are named either by their original image names (ImName) or FileName_SeriesNum_ImName

Reference

Based on Bio-Formats plugin, Bio-Formats Macro Extensions (called from Plugins menu of Fiji) and code examples from https://docs.openmicroscopy.org/bio-formats/5.8.0/users/imagej/