Open Microscopy Environment

Hello Everyone,

I have been looking for a way to convert .scn files (BigTIFF?) for SCN400 - the file type says Unix Executable File and about 1gig. A glimmer of hope has just appeared when I came across the Bio-Formats importer and exporter. When I try to import the files, which are scans of mouse knees up to 40x, the Import Options window pops up and I select View Stack With: Data Browser, Group files with similar names, and Use virtual stack. When I press OK, the File Stitching window pops up and I check the Pattern option with my file name and press OK.

The next window is the Series Options window - There are a total of 21 series. When I select multiple series or one of the series I have an Exception window pop up that says that the Array size is too large.

Ultimately, I would like to take the .scn files and convert them to a standard format with high quality for papers, presentations, to do cell counts and other quantifications with ImageJ. Is there some sort of tutorial that tells you how to convert .scn files?

Thank you for any support or input that you may have!

Sincerely,
Merissa

Hello Merissa,

Can I check how you are using Bio-Formats:
From within imageJ?
From within Fiji?

If imageJ you might need to allocate more memory to the application if you are working with very large pieces of data.

I will ask a colleague about this and get you a more full reply later.

Hope this helps,

Andrew

Hi Andrew,

I appreciate your quick reply! I am using this through ImageJ. I am very new to ImageJ, and any program in fact, and I do not quite understand how to allocate more memory.

- Merissa

Hi Merissa,

Instructions for allocating more memory to ImageJ are here:

http://imagejdocu.tudor.lu/doku.php?id= ... _in_imagej

However, given the nature of the data that you're working with, I would be surprised if that completely solves the problem. ImageJ can only open images when the size of each plane is smaller than 2 GB, regardless of how much memory is allocated; most full-resolution images in .scn files are substantially larger than that.

One option is to open individual tiles from the original .scn file and save each to its own file; the "Crop on import" option in the "Bio-Formats Import Options" window should allow you to specify the size and location of the tile to open.

The other option is to convert your files on the command line, which should convert the entire original .scn file to a single output file. Please see:

http://www.openmicroscopy.org/site/supp ... index.html

for further information on installing and using the command line tools (bfconvert is the one to use). Opening the converted file in ImageJ would still require using the "Crop on import" option.

If you encounter any problems with either of those options, please let us know and we'll do our best to help.

Regards,
-Melissa

Hello Melissa,

Thank you for your help! I am attempting to download the bftools but it's not working nor initiating the download. I will try again tomorrow.

Thank you!

- Merissa

Hi Merissa,

Have you been able to download bftools.zip? The direct link to the file is:

http://cvs.openmicroscopy.org.uk/snapsh ... ftools.zip

which is currently working for me. If you aren't able to download that or were attempting to download from somewhere else, please let us know.

Regards,
-Melissa

Hello Melissa,

I tried to download again today and it worked. I looked at the tutorial and I downloaded the file onto my desktop (it's a Mac) and downloaded the loci_tools.jar into the bftools folder. Am I supposed to put this entire folder into my imagej plugins? I do not know how to bring the command window up for bfconvert, do I need to import the image first?

Thank you so much for your help!

- Merissa