Thanks @DavidObe for sharing the EER file with us. Please can you also share with us
the job reports
- for the corresponding, single-GPU motion correction job
- and for the upstream Import Movies job.
Hi @DavidObe The motion correction event log indicates an error for a different EER file from the EER file you shared. Please can you share the file
FoilHole_29661719_Data_27198267_2_20241127_225634_EER.eer
with the developers as well as the job report for the corresponding Import Movies job.
Sorry for the delay on this. I investigated the file and I believe it is corrupt (but corrupt in an interesting way that I have not seen before, I will explain below). If the issue is confined to a single file, simply delete it and proceed with the rest of your data. If the issue is an entire dataset, something bigger must be wrong, possibly on the collection side.
The longer version:
The EER file format is (mostly ¹) an extension on top of the TIFF format. It relies on sneaking in extra metadata necessary for correct decompression in the “tag” system that is built into the TIFF spec. That metadata can take several forms but in the case of this file, it is XML data stored in the TIFF tag with tag number 65002. In this particular file, the metadata is present in all frames. In frames up to 283, the metadata seems to be correctly-formed XML and then starting at frame 284, the metadata abruptly becomes a sequence of null bytes. This causes the EER decoder to crash.
– Harris
¹ technically the spec permits a different container format other than TIFF, but in practice I’ve never seen it used - all EER files I’ve seen are TIFF