Regarding 4):
The macro below may help get you going. This macro was written to split
nii files (MRI scans), but you can modify it for your lif files. It
prompts for a directory, finds all nii files and for each creates a
directory and populates it with the z-stack as separate tif files. The
individual file names are specified by the SequenceParams variable - in
this case ³Š/slice_zXXX, where XXX is the 3-digit stack index.
If you need to also separate the channels you will want to add
³split_channels² to the BioFormatsParams variable, but then you will need
to add logic to save the separate channel images, either putting them in
separate directories or modifying the name. I would recommend that you
try the split by hand before running the macro. Open one of your lif
files with bioformats and then save using "File/Save As/Image SequenceŠ².
Good luck.
- Jim
The Jackson Laboratory
‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹
//
// This function expands an nii file into separate tif files, one per
z-layer
//
function split_nii(BaseDir, SampleName)
{
SampleFile = BaseDir + SampleName + ".nii";
DirName = BaseDir + SampleName;
BioFormatsParams = "open=" + SampleFile + " color_mode=Default
view=Hyperstack stack_order=XYCZT use_virtual_stack";
run("Bio-Formats Importer", BioFormatsParams);
File.mkdir(DirName);
SequenceParams = "format=TIFF name=slice_z digits=3 save=" + DirName;
run("Image Sequence... ", SequenceParams);
close();
}
//
// This function processes a directory of nii files.
// For each nii file a corresponding directory is created and
// populated with the tif files corresponding to the slices.
//
function ProcessDirectoryOfFiles(BaseDir)
{
write("Processing all nii files in directory: " + BaseDir);
FileList = getFileList(BaseDir);
for (i=0; i<FileList.length; i++)
{
if (endsWith(FileList[i], ".nii"))
{
write(" " + FileList[i]);
SimpleName = replace(FileList[i], ".nii", "");
split_nii(BaseDir, SimpleName);
}
}
write(" Done");
}
function main()
{
setBatchMode(true); // prevent the
image window
write("Select directory containing nii files..."); // Write a prompt
to the log window
BaseDir = getDirectory("."); // Pop up the file
select dialog
ProcessDirectoryOfFiles(BaseDir); // Process all nii
files in the directory
}
main();
‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹
On 2/5/18, 3:42 PM, "ImageJ Interest Group on behalf of csadangi"
<
[hidden email] on behalf of
[hidden email]> wrote:
>Hi,
>
>I have a few questions:
>1) I am using a Leica Confocal SP8 and the files are .lif. When I drag the
>experimental file to ImageJ, it opens up a console with warning (attached
>screenshot). Will it affect my images in any way?
><
http://imagej.1557.x6.nabble.com/file/t379887/1.gif>
>2) I also get a Bio-format option but I just click ok with the default
>settings. Should I change anything? (attached screenshot)
><
http://imagej.1557.x6.nabble.com/file/t379887/2.jpg>
>3) Once I open a series, it only shows up as blue in color. But while
>imaging, I used blue, green and red channels. How can I view them in their
>original channels?
>4) Is there a way to extract each image as a separate file using ImageJ? I
>took over 30 images and some z-Stacks, can I save them as individual
>files?
>
>5) I want to calculate the fluorescence intensity at the membrane. I
>found a
>paper describing the same but I am unclear as how to calculate the peak
>intensity. I have attached a screenshot for the same
><
http://imagej.1557.x6.nabble.com/file/t379887/3.jpg> .
>
>My specific questions are:
>a) How did they draw two lines in the image. I drew one line and clicked
>draw, but when I tried to draw the second line the first line disappeared.
>b) What do they mean by 2 values/line?
>c) How did they calculate the distance?
>d) Is the distance between peak 1 and peak 2 the fluorescence intensity?
>e) Should I just measure the center of the circle to calculate the
>intensity?
>The link to the complete paper is here:
>
https://elifesciences.org/articles/28270/figures>
>Thank you in advance for helping me.
>
>
>
>-----
>----
>Chinmaya
>Medical University Innsbruck
>Innsbruck
>Austria
>--
>Sent from:
http://imagej.1557.x6.nabble.com/>
>--
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