Crop Cells (Big Data)

The tool allows to crop cells in very large time-series of image files. It expects projections of the files in one folder and the complete time-series in another folder. The user can define regions of interest on the projections and the corresponding images will be cropped time-step by time-step to the regions.

Getting Started

Drag the link crop_cells_big_data_series.ijm onto the ImageJ launcher window, save it under macros/toolsets in the ImageJ installation and restart ImageJ.

Select the "crop_cells_big_data_series" toolset from the >> button of the ImageJ launcher.

the crop cells toolset

  • the button with the crop-symbol opens this help page
  • s allows to make the selections of the regions that will be cropped using the projections of the original images
  • c will crop the original time-series files to the regions defined before


Right-click on the s-button to open the options dialog.

  • name of the TimeLapse folder: part of the name of the folders containing the time-series
  • name of the projection folders: name of the subfolder of the TimeLapse folders that contain the projections
  • part of the name of the MIP files: a part of the filename of the projection files used to filter out other files that might be in the folder
  • file extension: the file extension of the image files (for example .tif)

toolset.png - the crop cells toolset (814 Bytes) Volker Baecker, 04/04/2017 03:18 PM

Options.png (10.1 KB) Volker Baecker, 04/04/2017 03:24 PM