Thank you for the reply about RAM. This is an important consideration, but not the source of the problem.
For a different experimental system we routinely open 60 GB nd2 data files (single channel, many timepoints, full field from a Zyla 5.5 camera), so RAM setting should not be the problem. We've tried this on 3 different PCs and one of the labs that has the same problem with a different camera on a Nikon system uses Macs. Also, we don't have this problem with tiled lightsheet multichannel volumes in czi format. Cheers- Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory NYU Langone Health, New York, NY 10016 [email protected] http://nyulmc.org/micros http://microscopynotes.com/ Cell voice (no text) 1-914-309-3270 Office 1-646-501-0567 ________________________________ From: Michael Schmid <[email protected]> Sent: Tuesday, March 12, 2024 4:57:57 AM To: [email protected] Subject: Re: Problem opening large ND2 files in ImageJ [EXTERNAL] Hi Michael, the problem with image size is probably related to the memory you have allocated to ImageJ. ImageJ has a limit for the number of pixels in an image of 2^31 - 1, roughly 2.14e9. Your image size is 58157 x 33163 = 1.93e9, so in principle it should be possible to open it. With 4 channels, 2 bytes each, the image needs 14 GB of memory, plus 7 GB (4 bytes/pixel) to display it. If you want to do any operations on the image you will need more memory. I think that 32 GB RAM with 30 GB or so allocated to ImageJ (if no other program is open) would be the minimum for very basic operations; many operations will need more. Michael ________________________________________________________________ On 11.03.24 18:10, Cammer, Michael wrote: > We are wondering whether anybody has solved the following problem? > > > We have time lapse images of a few fields of stitched images and also still > images of much larger stitched images (whole mouse brain slices) generated > with Nikon Elements which we cannot open in Fiji. We have tried both > BioFormats 6.5.0 and 7.2.0. > > > The error we get is "Unsupported format or file not found." > > > When ND2 did not work, we tried exporting to tif files. We have tried both > separating the channels to generate smaller single channel images and saving > at OME TIFF. Both yield the same error message. > > > We did try cropping the largest of our images, 58157 x 33163 pixels, exactly > in half, but this will not open too (29078 x 33163 pixels, 4 16 bit > channels). We tried cropping out a small area, 2000 x 2000 pixels, and this > does open ok. We need two of the 4 channels in 16 bits, so we did not try > converting to 8 bits. > > > This led us to the question, what is the largest image that BioFormats in > ImageJ will open from a Nikon Elements generated dataset? Have we hit a > ceiling? > > > Any help would be appreciated. > > > Best regards- > > > Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory > > NYU Langone Health, New York, NY 10016 > > [email protected]<mailto:[email protected]> > > http://nyulmc.org/micros http://microscopynotes.com/ > > Cell voice (no text) 1-914-309-3270 > > Office 1-646-501-0567 > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
