Dear Michael, There is an ND2 plugin at https://imagej.net/ij/plugins/nd2-reader.html that might solve the problem. There were some reports in the past that it only works in ImageJ but I just tested it and it works in Fiji as well. However, it only has a windows installer and has to be installed in the Fiji folder. Under plugins you get NDi6d
Best wishes Kees Advanced Imaging Facility (RRID: SCR_020967) University of Leicester www.le.ac.uk/advanced-imaging-facility<http://www.le.ac.uk/advanced-imaging-facility> ________________________________ From: Cammer, Michael <[email protected]> Sent: 11 March 2024 17:10 To: [email protected] <[email protected]> Subject: Problem opening large ND2 files in ImageJ [Some people who received this message don't often get email from [email protected]. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] ***CAUTION:*** This email was sent from an EXTERNAL source. Think before clicking links or opening attachments. 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]> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fnyulmc.org%2Fmicros&data=05%7C02%7Ckrs5%40leicester.ac.uk%7C9457d542a1384b15791708dc41ee7fb3%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C0%7C638457739803711001%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=43dKciewOa8IxxZzX3Hm8GHQ7aKHNaHcGcj4bQaK8f0%3D&reserved=0<http://nyulmc.org/micros> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmicroscopynotes.com%2F&data=05%7C02%7Ckrs5%40leicester.ac.uk%7C9457d542a1384b15791708dc41ee7fb3%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C0%7C638457739803719240%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=gkEKtTIZqmYRBmOz69d36AsohAoICYh2OdFoB%2BvnP3k%3D&reserved=0<http://microscopynotes.com/> Cell voice (no text) 1-914-309-3270 Office 1-646-501-0567 -- ImageJ mailing list: https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.nih.gov%2Fij%2Flist.html&data=05%7C02%7Ckrs5%40leicester.ac.uk%7C9457d542a1384b15791708dc41ee7fb3%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C0%7C638457739803725292%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=Ucz6CPIemu2c4cqnV2Zv%2FejOEEgFZzYH6AMTTJCAZHI%3D&reserved=0<http://imagej.nih.gov/ij/list.html> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
