Dear Ralph
We have had a similar problem. The Biorad file (as I remember it
-others please correct if I'm wrong) has a 512 byte header with lots
of info about the picture etc. To translate the file from Zeiss tiff
you will have to read the Zeiss header to get the resolution info etc.
I have a Zeiss but I don't have the information on the Zeiss header.
Perhaps someone else in the group has this info. in which case I would
like it for future reference also. In any case, a special prgram will
probably have to be written (by someone) to create a pic. file...
Hi there,
Although I am not aware of any "elegant" solution to the problem of converting several TIFFs to a single Bio-Rad PIC file under DOS/Windows, there is a *TEMPORARY* workaround that I can suggest:
1) Put all TIFF files relating to a confocal stack into a separate directory. Batch convert all TIFF files to RAW format using a program such as PaintShop Pro (Windows) or Display (DOS). The input TIFF files should be simple 8-bit grayscale images, and the output files should be 8-bit, 1-byte per pixel.
Links to these programs can be found on my PC Software page at:
http://www.cs.ubc.ca/spider/ladic/softibm.html
2) concatenate all of the RAW image files togther using the DOS COPY command:
COPY /b *.RAW temp.pic
..this assumes that all of the files are ordered (i.e. in ascending order, most likely with a number appended to the file name.) The /b switch ensures a binary file copy such that no carriage return will be added to the end of the files when they are concatenated.
3) add a *76-byte* Bio-Rad header to the now single PIC file. I could supply a "default" dummy header that you could modify to suit your data set. Basically, only bytes 0-4 of the file have to be modified to reflect the X*Y size of your images and the total number of images, everything else can be left as is. See the brief description of the Bio-Rad header format at my Web site on the following page:
http://www.cs.ubc.ca/spider/ladic/fileform.html#BIORAD
Say the 76-byte header file was called "header":
COPY /b header+temp.pic stack.pic
...the "stack.pic" file would then include the necessary header plus all of
your image files.
Doing all of this on a Unix platform would be trivial by making use of a command line program like ImageMagick which could do the image conversion and a simple script/C program. Unfortunately, I do not currently have ready access to many programming tools under DOS/Windows, or I could put something together for you there.
I haven't actually tested the above properly yet, but if you are interested, let me know, and I will actually test it out with some simple data, and/or put up a simple "dummy" header on my Web site that you can download and use.
Lance Ladic
ladic@CS.UBC.CA
Recently there have been some questions regarding the use and conversion of files to the Bio-Rad PIC image format for use with the program Confocal Assistant.
To clarify a couple of points:
The Bio-Rad PIC file format utilizes the ability to store a Z series or time series as a single file. The PIC file itself consists of a 76 byte header followed by a pixel array of NX x NY x Npic bytes where NX and NY are X and Y pixel dimensions of the image and Npic is the number of images in the file.
The format of the Bio-Rad header is available from the CoMOS reference section of the users manual. Further information about the Bio-Rad PIC file format itself, is available to Bio-Rad Confocal users upon request, from myself.
Further user information on the Bio-Rad PIC file format and how to convert it to other formats can be found at the following web page maintained by Lance Ladic, University of BC Canada:
http://www.cs.ubc.ca/spider/ladic/confocal.html
and then select the Source Code & Tips icon.
Andy Sowerby
e-mail andrew_sowerby@bio-rad.com