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ImageJ Bioformats 8.3.0 Importer Incorrectly Reading ND2 Metadata

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Zenodo2025-08-21 更新2026-05-26 收录
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Hi all,I was referred to this community from the Image.sc Forum original post: https://forum.image.sc/t/imagej-bioformats-importer-incorrectly-reading-metadata/115943 I have an ND2 file, 3 color channels, 2 positions in the well, and 81 timepoints. However, when I open this as I normally would in ImageJ as a hyperstack, the stack interpretation is totally incorrect. It is including my Z-positions as frames in the timelapse. Even when I open the series for the positions independently, images from the other series will appear within it. I am running Bioformats 8.3.0. I have tried swapping dimensions. That did not work. I have tried creating substacks to parse out one series from the other, this also did not work. The only thing I can think of that is different from before is that I was previously aquiring z-stacks with our MCL nanodrive Piezo, and we had to have that serviced so in the meantime I used the Ti2 eclipse camera drive for z-stack aquisiton. I have opened the metadata to compare aquisitions between the two, and the stack order appears exactly the same, although Bioformats has no problem reading the metadata for aquisitions with the Piezo. I have also opened this file in NIS elements viewer, and all the information for the stacks appears correctly, so I dont think aquisitions is the issue. I have also tried opening this file on multiple computers with multiple versions of imageJ, and the issue persists. Any advice would be greatly appreciated I am panicking a bit because this is a few months worth of data I am suddenly not able to analyze. Please let me know if there's anything else needed to help figure this out.

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Zenodo
创建时间:
2025-08-21
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