Take the 2-minute tour ×
Biology Stack Exchange is a question and answer site for biology researchers, academics, and students. It's 100% free, no registration required.

I asked a related question on SO, but I also had some biology related questions to this issue.

One of the big things I'd like to do is sort between DNA/UV images and Western/Chemi images. After manually scrolling through the hex of a few of these files, I think the section that might help me with this information is here:

filter region of .1sc hex

My logic is that the imageing_mode and filter will be the best way to determine this information. Again, as in my SO question, I don't know how to decode them, but there should only be three imageing_modes in the whole set, so I might be able to manually map them.

I also found the information directly spelled out in the hex: Chemi notation in .1sc

But it actually seemed a little more problematic to use. In the 10 files I've looked at manually, this information is at a different place each time. There doesn't seem to be a pattern in the placement of UV vs. Chemi. It's true that I could try and parse the whole file, but I think that would take way too much time. The imaging mode part does seem to be in the same place, so if I could use that it would be preferable.

Is there a better meta-element to be looking for? I'm confused as to why the Chemi text is in a different location between files. It doesn't seem to be after the actual image information, but maybe I'm missing the image lead in. Doe anyone know what actually indicates the start of the image?

Does anyone know if there is a better way to make this determination with information that is already being processed with ImageJ? Alternatively, is there a better software suit to batch process large amounts (3T) of .1sc files? My attempts at using QuanityOne and ImageLab have crashed and led to fragmented output.

share|improve this question
Maybe shoot an email to BioRad Tech support? (I'm guessing the metadata's non-zero bytes that follow the variable name are numerical or character values. I also doubt the data is actually encoded in Intel Hex but I checked your SO data (typos corrected) against all 73 character encodings in Mathematica and no obvious answers jumped out.) –  PlaysDice May 29 at 15:16
but every 'metadata' entry takes the form VARIABLE_NAME 0, 10, 0 ... –  PlaysDice May 29 at 15:20
It is a biorad proprietary file format. I don't really know what the fields mean. If has text data and you know what the fields are then it would be easy to analyse using commandline functions. I would recommend that you either export the file into a format that is readable by other programs or use biorad recommended software. –  WYSIWYG May 29 at 16:32
@PlaysDice I had noticed that pattern as well. I've sent a request in to Bio-Rad, I know that they shared information about the format to NIH for ImageJ, I don't know if they will readily hand it out. I also don't know if the BioFormats group would be able to do it with the info they have, but haven't based on priority. –  Atl LED May 29 at 16:37
@WYSIWYG I understand that .1sc is still under protection. They have shared information about the format with the public domain, and I'm uncertain how extensive that sharing has been. The general goal is to export a large batch of files into a more accepted format, I was just hoping to capture more information from the file. My attempts at using BioRad's software on such a large set have failed so far. –  Atl LED May 29 at 16:41

Your Answer


By posting your answer, you agree to the privacy policy and terms of service.

Browse other questions tagged or ask your own question.