Posted by
Hoover, Karl on
Mar 25, 2011; 8:03pm
URL: http://imagej.273.s1.nabble.com/LOCI-Hamamatsu-HIS-file-tp3685250p3685252.html
This is a good scenario for trying out a 64 bit operating system.
________________________________________
From: ImageJ Interest Group [
[hidden email]] On Behalf Of popilika [
[hidden email]]
Sent: Friday, March 25, 2011 11:21
To:
[hidden email]
Subject: LOCI Hamamatsu HIS file
I did a high speed image streaming through a hamamatsu image acquisition
software. The program automatically stacked all the images and save them
onto a single file with an extension 'HIS'. HIS file can be opened with the
LOCI bioformat importer with minor glitches, as my average filesize tends to
be around 2GB or more (~2,000-4000 images per file). All I am trying to do
is to split the all the images in the stack and save them all to either tif
or Jpg format in a seperate folder.
The trouble is, I can't open them all at once as this would eat up all the
virtual memory i have on the computer. I'm quite new to Fiji and not
particularly familiar with JAVA syntaxes or ImageJ built-in macro functions.
I went through a fair few descriptions of some of the functions as well as
learning from some of the pre-written macros on the the LOCI official
website
http://www.loci.wisc.edu/bio-formats/imagej. There's an example file
on there which sort of do a similar task called 'recursivetiffconvert'. The
macro supposes to convert all DM3 files in a directory and then batch
convert them to tiff format. I tried the code and pointed it to read HIS
file instead of DM3. At first, it seems to be loading all the images in
background under the 'setBatchmode command' (am I right to assume that?), as
my hard disk just screamed upon an execution. However, in the end, it only
saved either the last or the first frame of HIS stack into tiff. I went
through the bioformat macro-extension to see if there is any sub-routines
which i could call after 'run("Bio-Formats Macro Extensions");' to count the
total number of files and then do the block conversion in the background.
Embarrassingly I'm dead after the first few lines. Had a string of Java
errors, it said that the conflict was caused by illegal/unsupported escape
sequence I only know some programming in matlab. Could anyone please point
me out to the right direction? This is my super basic code. Please go easy
on the terminologies, I'm super new. Thanks very much.
//Get directory for HIS images
hisDir = getDirectory("Choose HIS images ");
hisList = getFileList(hisDir);
hisim = hisDir+hisList[0];
print(hisim);
run("Bio-Formats Macro Extensions");
fileID = Ext.setId(hisim);
setBatchMode(true);
//somehow get the total number of images, create a loop and do block
loading/coversion in the background.
setBatchMode(false);
http://imagej.588099.n2.nabble.com/file/n6208708/Clipboard01.jpg--
View this message in context:
http://imagej.588099.n2.nabble.com/LOCI-Hamamatsu-HIS-file-tp6208708p6208708.htmlSent from the ImageJ mailing list archive at Nabble.com.