The Leica confocal saves images as indexed color unless you follow the procedures described in saving images.




Jennie Dorman has written instructions for working on the Mac with Leica files using ImageJ.


ImageJ

The program can be downloaded free from http://rsb.info.nih.gov/ij



Adobe Photoshop

Files from the "new" software can be read directly into Adobe Photoshop.



Adjust the contrast/brightness of an image using Adjust|Levels


Adjust each color individually

Use the upper arrow in input levels to "stretch" the intensity levels i.e.make the label brighter.

Use the lower arrow to decrease/increase the threshhold or offset.

Use the middle arrow to adjust the gamma or intermediate levels. This will make the intensity levels nonlinear.

Before printing, or for publication, change the resolution (DPI) in Photoshop. Don't use other programs to change the resolution, they don't do it as well as Photoshop and quality is often lost in this step.

Images are collected at 72 dpi.

Changing to at least 144 dpi will avoid that "pixelated" look in the image.

Change the resolution under Image|Image Size... Constrain Proportions should be checked. Resample Image should also be checked and bicubic.



Leica Converter: Leica converter will take a ScannerFile z-series from the "old software" and split it into individual files. It runs on a PC.

Images must be saved in color to use this program i.e.channel one in green, channel two in red and channel three in blue.

Double click on the Leica converter icon on the desktop.

Click on File and Open to open the Leica scanner file to be converted.

Select an option:

Intensity coded (w/o LUT) saves each image as grayscale.
Color coded (with LUT) saves each image as an indexed color.
Color overlay saves each series as an RGB image.


Click on File and Save as...

Give the file a different name and save it.



Scion Image

The program can be downloaded free from http://www.scioncorp.com

It runs on a PC - use NIH-Image for the MAC.



ImageTool

The program can be downloaded free from http://ddsdx.uthscsa.edu/dig/

It runs on a PC - use NIH-Image for the MAC.



MetaMorph

MetaMorph is a powerful image analysis program that will open Leica images.

Among the many features of the program:

"Rebuild" a stack of images
Project a stack of images
Unmerge (separate) an RGB image
Correct an uneven background
Overlay a fluorescent and transmitted (DIC) image
Merge (color combine) images
Sharpen images (don't overdo)
Align channels (2p + confocal)

It runs on a PC - use NIH-Image for the MAC.



NIH-Image

The program can be downloaded free from http://rsb.info.nih.gov/nih-image/download.html

Mac only



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