Make Montage with ImageJ: create gallery from stack
open ImageJ
open image stack: File>Import>Image Sequence
n the following dialog, choose the appropriate parameters (starting image actually refers to the number of the first file in the folder, which is not necessarily an image (like in LEICA LCS files/folders; therefore skip the *.lei and *.txt file by starting with "image" #3)
go to menu Image>Stacks>Make Montage
TurboReg ImageJ plugin: batch registration of images in an image stack
Open ImageJ
Check if the Turboreg plugin from P. Thevenaz (URL: http://bigwww.epfl.ch/thevenaz/turboreg) is located in the plugins menu. Otherwise you or your admin should install it. (Close and restart ImageJ after installing plugin to make the plugin active)
Open image stack: File>Import>Image Sequence
In the following dialog, choose the appropriate parameters (starting image actually refers to the number of he first file in the folder, which is not necessarily an image (like in LEICA LCS files/folders; therefore skip the *.lei and *.txt file by starting with "image" #3) Caveat: if there are mre than 1000 images in one channel or time series, the sequence of readig images into a stack is different for LCS and ImageJ software (you have to rename - ask Günter Giese)
Scroll through the stack. Choose a reference image for the alignment procedure
Make a copy of this reference image: Image>Duplicate (leave the checkbox "Duplicate Entire Stack" unchecked)
Open the turboreg plugin: Plugins>turboreg>TurboReg
Set the parameters as desired - an example:
To start alignment, press the Batch button. A new stack named Registered will be created which represents the registered stack
Convert images to 8bit in ImageJ (if starting images were 8 bit)
