In article <[log in to unmask]> Dr M Cannell <[log in to unmask]> writes:
>Date:         Tue, 23 Jan 1996 15:00:53 PST
>Reply-To: Confocal Microscopy List <[log in to unmask]>
>From: Dr M Cannell <[log in to unmask]>
>Subject:      Re: converting TIFF to biorad .pic series
>To: Multiple recipients of list CONFOCAL
 
>On Tue, 23 Jan 1996 14:41:36 +0100 Ralf Steinmeyer wrote:
 
 
>>
>> I have just tried the Program Confocal Assistant. As I understand
>it, to
>> work with series in Confocal Assistant a single .pic file has to
>contain
>> the whole series. Our ZEISS Confocal Microscope saves z-series as
>TIFF files
>> with one single image of the series in each file, so I think they
>have to
>> be connected to one .pic file.
>>
>> Does anyone know how to convert TIFF files taken as a z-series with
>a
>> ZEISS Confocal Microscope to a Biorad .pic file?
 
>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.
 
Regards,
 
--Lance.
-------------------
Lance Ladic
Dept. of Physiology
University of B.C.
Vancouver, Canada
-------------------