Modules

Save image

Save an image/stack from the workspace to file.

Description

Save an image/stack from the workspace to file. These files can be placed in the same folder as the input file, located in a specific folder or placed in a directory structure mirroring the input structure, but based at a new location. For greater flexibility in output file locations and filenames, the "Save image (generic)" module can be used. To prevent overwriting of previously-saved files, the current date and time can be appended to the end of each filename. Images can be saved in a variety of formats (AVI, TIF and Zipped TIF).

Parameters

Parameter Description
Save location Select where the image should be saved.
  • "Mirrored directory" Save the image to a new directory structure which has the same layout as the input. This is useful when batch processing from a multi-layer folder structure. The subdirectory layout will match that of the input structure, but will have its root at the folder specified in "Mirrored directory root".
  • "Match Output Control" Save the image to the folder specified by the "Save location" parameter in "Output control".
  • "Save with input file" Save the image in the same file as the root file for this workspace (i.e. the image specified in "Input control".
  • "Specific location" Save the image to a specific folder.
Mirrored directory root The root path for the mirrored directory structure. This path is the equivalent of the folder specified in "Input control". All subfolders will be in the same relative locations to their input counterparts.
File path Path to folder where images will be saved.
File name (generic)
Save name mode Controls how saved image names will be generated.
  • "Match input file name" Use the same name as the root file for this workspace (i.e. the input file in "Input control".
  • "Specific name" Use a specific name for the output file. Care should be taken with this when working in batch mode as it's easy to continuously write over output images.
File name Filename for saved image. Care should be taken with this when working in batch mode as it's easy to continuously write over output images.
Append series mode Controls if any series information should be appended to the end of the filename. This is useful when working with multi-series files, as it should help prevent writing files from multiple runs with the same filename. Series numbers are prepended by "S". Choices are: None, Series name, Series number.
Append date/time mode Controls under what conditions the time and date will be appended on to the end of the image filename. This can be used to prevent accidental over-writing of images from previous runs:
  • "Always" Always append the time and date on to the end of the filename.
  • "If file exists" Only append the time and date if the results file already exists.
  • "Never" Never append time and date (unless the file is open and unwritable).
Add filename suffix A custom suffix to be added to each filename.
Input image Image to be saved to file.
File format The format the output image will be saved as:
  • "AVI" Video written using the stock ImageJ "AVI Writer". Videos can use different compression algorithms specified using "Compression mode". Framerate specified by "Frame rate (fps)" parameter.
  • "TIF" Standard multidimensional (multi-page) TIF image saving.
  • "ZIP" TIF images stored using ZIP compression. For images with large homogeneous regions of pixel intensity this can greatly reduce file size in a lossless manner. Zipped images can be read directly back into ImageJ/Fiji without the need for prior decompression.
Channel mode Control whether saved images should be in ImageJ "Composite" (display all channels simultaneously) or "Color" (display one channel at a time) mode.
Save as RGB Convert images to RGB prior to saving. This is useful for displaying multi-channel images to a format that can be easily viewed outside ImageJ.
Compression mode Compression mode used when saving AVI videos ("File format" parameter):
  • "JPEG" Lossy video compression with quality specified by "Quality (0-100)" parameter. This option is good when reducing video size is more important than retaining perfect image quality.
  • "None" Frames are stored in their raw format (uncompressed). This gives the highest quality, but also the largest file size.
  • "PNG" PNG video compression.
Quality (0-100) Quality of output JPEG-compressed video (values in range 0-100). For reference, saving AVIs via ImageJ's "File > Save As..." menu uses a quality of 90.
Frame rate (fps) Output video framerate (frames per second).
Flatten overlay Flatten any overlay elements onto the image prior to saving.