wisamreid / arrangechannels-stacktotiff Goto Github PK

this macro is intended to convert the z-stack, multichannel images from .lif files into
individual tif files in a batch method. 

After (or before) starting this macro, bring the .lif file to imageJ and open all of the
images you want to save as individual tiff files. It will have a popup asking you to do
this as well.

It will ask  you to select a folder to save the individual .tiff files in.

The default options are:

"co-culture"
	four channels in the original uncompressed image
	z stack original image
	not compressed to RGB format for final image
	Arrangement of channels is 1-Cyan, 2-Blue, 3-Green, 4-Red
	1024x1024 images	

"normal E18"
	three channels in the original uncompressed image
	z stack original image
	Compressed to RGB format for final image
	Arrangement of channels is 1-Green, 2-Red, 3-Blue
	1024x1024 images	

"a-synuclein project"
	four channels in the original uncompressed image
	z stack original image
	not compressed to RGB format for final image
	Arrangement of channels is 1-Cyan, 2-Blue, 3-Green, 4-Red
	2048x2048 images

"Custom"
	lets you modify each of the parameters listed above (except image size)
	asks for:
	-initial # of channels
	-# of channels desired in final image
	-whether or not the final image should be flat
	-if you want to add a suffix to all of them (ex: "...tif_flat")
	-which color is in which channel
	-which colors/channels should be in the final image
	-if you want to change the color of individual channels (ex: cyan->blue for an 
	RGB final image)

Once the parameters are set, it will go through the open images and ask you to rename them.
This is to remove the .lif filename from the individual image name if desired. 
If you want to keep the .lif filename, just hit "ok" until all of the images are
processed.

Each image will be proccessed in the same way. The purpose of this is to expedite
image import from .lif files and allow for modification of said images in a customized
and consistent way without manually doing it.

frequently used in image analysis done for multiple projects - useful for
a broad range of applications.