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 -------------------