Wes,

Many programs have a raw import method that can be used to grab the data out
of a proprietary file format.  The trick is to know the array size and bit
depth of you images as well as how many images are in your stack.  As an
example a 512 x 512 stack of 10, 8 bit images, should have a size on disk of
(512 * 512 * 10 *8) = 20971520 bits, or 2621440 bytes.  So if your stack
file has a size of 2621450, it has a 10 byte header.

You mention .stk files.  Are you by change using MetaMorph?  If so, Meta has
a built in importing utility that simply asks for the bit depth of the image
to be imported the height & width, number of planes and offset (i.e. header
length).  It may take a few iterations to figure out the header size
correctly, but fortunately, any errors are glaringly obvious, so it is easy
to find the correct header length by simple repetition.  Most program and
file types always use the same header, so once you figure out the header
length, you shouldn't need to do so again.

Chris Tully
Digital Imaging Specialist

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-----Original Message-----
From: Confocal Microscopy List
[mailto:[log in to unmask]]On Behalf Of Wes Wallace
Sent: Sunday, April 23, 2000 6:07 PM
To: [log in to unmask]
Subject: file format conversion


Is there any kind of software package out there which simply converts 3D
image files from one format to another?  I find that the selected formats
handled by various packages always somehow leave out the one format in
which the two packages could talk to each other.

I gather that all monochrome 3D image files share a fairly similar
structure in that the data is represented as a series of pixel brightness
values.  However, the x/y/z dimensions of the file and other mysterious
information are encoded in the header, and each software package,  uses a
completely unique header format which the other packages can only read if
their companies are on good terms with each other.

The formats I work with the most are STK, TIF (as numbered series of 2D
files) and BIN (I think this is the most stripped down format,
corresponding to just the pixel values without any header at all).  If
there was one program which could reside on multiple machines and simply
convert these three formats one into another, as well as swap byte order
if necessary, this would really be a godsend.

I'm certain that the program would be incredibly simple to write, but I am
incredibly ignorant about the details of file formats.  (In fact some of
the details are proprietary information if I understand correctly.)

Wes Wallace
Department of Neuroscience
Brown University
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