Opening Series of Images to Layers or Z Project Confocal Images

How to open an image series (image sequence) in Photoshop for those who use confocal or widefield microscopes and take z-sections or time course. If images are from a confocal, it’s best to do steps in Image J (see Merging Fluorescent Images in Image J).

How to Open Image Series (image sequence) in GIMP

An image sequence in GIMP is generally done to subsequently create a GIF animation
1. File > Open as Layers
In Open Image box select all images from the image sequence
2. Optional: Image > Scale Image (to make smaller dimensions)
Specify image size in box in pixels
Cubic Interpolation
Click Scale
3. File > Export (to create GIF animation)
Put a “.gif” at end of file name
In next dialog box, if you want a continuous play, check Loop
Set delay at 12.**
*Image sizes are often too large for web output if images are too large (greater than 800 or so pixels in any dimension).
** Re-export if a delay of 12 is too slow or too fast and add delays iteratively.

Open Image Sequence in Image J

  1. File > Import > Image Sequence
  2. Select only the first file (001) in the image sequence
  3. Edit > Options > Appearance (set appearance to bit depth of images)

Open Confocal Series in Image J

File > Open*
In dialogue box click Virtual Stack (other settings can remain unchecked)
Edit > Options > Appearance (set appearance to bit depth of images)
* It’s assumed the opened file is in the manufacturer’s format (e.g. “.oib”)

See the Instruction Page for an index of all instructional videos and documents
See Image Ethics for image integrity information on how to avoid scientific misconduct

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