We just switched to using Andor/Bitplane Fusion software to acquire images on our Dragonfly confocal. Fusion saves out images automatically as .ims files (which apparently are slightly different than actual .ims files from Imaris due to lack of compression). These .ims files can be loaded into ImageJ/FIJI with Bioformats just fine, but it is quite slow compared to loading a similar size multi-page TIF file. Fusion can export OME-TIFs, but only a single image-stack at a time, which is really not ideal if you’re taking a lot of images. Is anyone familiar with a faster or better way to import .ims files from Fusion into FIJI?
Not sure if it’s going to help but just to let you know you can convert Dragonfly .ims files to “normal” .ims files using the Imaris File Converter. From my experience I don’t think it’s going to make opening the files any faster but I’ve never actually tested it.
Imaris files are pyramidal and you’ll have noticed Bio-Formats lets you choose which series resolution level you want to open, perhaps depending on what you are needing to do with the file, maybe you don’t always need the full resolution?
Another thing to look into would be BigDataViewer for opening the files as I’ve always found it opens .ims files very quickly.
And finally, you could look into converting the files using the Bio-Formats command line tool bfconvert. This would allow you to convert the .ims file into a multi-dimensional ome-tiff.
Any of the recommendations from Laura are worth trying. If converting to an OME-TIFF using the bfconvert tool then it might be worth looking at the options for pyramidal resolutions so that the converted file has the correct resolutions that you require.
I wrote a macro that calls the BioFormats plugin in Fiji (most recent version) and imports the highest spatial resolution version of the dataset in the .IJM file (no conversion to “plain old” .IMS), with is called “Series 1” or something like that. I gave it the option of loading as a Virtual HyperStack (fast) or into RAM (slow, as you describe). The problem with Virtual Stacks, which I’ll post in a separate thread, is that for me there is a weird autothresholding/contrast enhancement occurring that makes the Virtual version unusable for now. I’m hoping the BioFormat folks can look at it.
Jeff Hardin, Dept. of Integrative Biology, Univ. of Wisconsin-Madison
Thanks for the feedback everyone, I’ll definitely look into some of these options. I had also written an ImageJ macro for opening the ims file directly in FIJI with the highest resolution, which is fine. I just wish it wasn’t slow. I had tried playing with the imaris file converter option, but as suggested that didn’t make a difference for speed. BigDataViewer opened the files quickly, though I wasn’t sure how to then use files in that mode with my usual ImageJ/FIJI analysis macros, but I also didn’t try that hard.