If you think you have found a bug in Bio-Formats, the first thing to do is update your version of Bio-Formats to the latest version to check if the problem has already been addressed. The Fiji updater will automatically do this for you, while in ImageJ you can select Plugins ‣ Bio-Formats ‣ Update Bio-Formats Plugins.
You can also download the latest version of Bio-Formats. If you are not sure which version you need, select the latest build of the Bio-Formats package bundle from the components table.
If your 12, 14 or 16-bit images look all black when you open them, typically the problem is that the pixel values are very, very small relative to the maximum possible pixel value (4095, 16383, and 65535, respectively), so when displayed the pixels are effectively black. In ImageJ/Fiji, this is fixable by checking the “Autoscale” option; with the command line tools, the “-autoscale -fast” options should work.
If the file is very, very small (4096 bytes) and any exception is generated when reading the file, then make sure it is not a Mac OS X resource fork. The ‘file’ command should tell you:
$ file /path/to/suspicious-file suspicious-file: AppleDouble encoded Macintosh file
If you get an OutOfMemory or NegativeArraySize error message when attempting to open an SVS or JPEG-2000 file then the amount of pixel data in a single image plane exceeds the amount of memory allocated to the JVM or 2 GB, respectively. For the former, you can increase the amount of memory allocated; in the latter case, you will need to open the image in sections. If you are using Bio-Formats as a library, this means using the openBytes(int, int, int, int, int) method in loci.formats.IFormatReader. If you are using Bio-Formats within ImageJ, you can use the Crop on import option.
Note that JPEG-2000 is a very efficient compression algorithm - thus the size of the file on disk will be substantially smaller than the amount of memory required to store the uncompressed pixel data. It is not uncommon for a JPEG-2000 or SVS file to occupy less than 200 MB on disk, and yet have over 2 GB of uncompressed pixel data.
If you can still reproduce the bug after updating to the latest version of Bio-Formats, and your issue does not relate to anything listed above or noted on the relevant file format page, please send a bug report to the OME Users mailing list. You can upload files to our QA system or for large files (>2 GB), we can provide you with an FTP server address if you write to the mailing list.
To ensure that any inquiries you make are resolved promptly, please include the following information:
Please be patient - it may be a few days until you receive a response, but we reply to every email inquiry we receive.