Recover Corrupt ISXD Movie¶

This tool uses 0.5 compute credits per hour.

This tool recovers corrupted ISXD movie files.

Inputs¶

Parameter	Required?	Default	Description
Movie File	True	N/A	The isxd movie with corrupted metadata to recover.
Start Time	True	auto	Start time to set for the output movie. Timestamps must be in ISO 8601 format: YYYY-mm-dd HH:MM:SS.ffffff. If 'auto', the date time is inferred from the movie file name to the nearest second. If a date time cannot be inferred from the file name, the current date time is used wtih UTC time zone.
Sampling Rate	True	20.0	The sampling rate in Hz to set for the isxd movie.
Width	True	1280	The width of the input movie. It's important that this value matches the actual width of the input movie in order for frame data to be correctly copied to the recovered movie.
Height	True	1080	The height of the input movie. It's important that this value matches the actual width of the input movie in order for frame data to be correctly copied to the recovered movie.

File Inputs¶

Source Parameter	File Type	File Format
Movie File	miniscope_movie, unknown	isxd, isxd

Background¶

File corruption usually happens due to one of the following reasons:

A recording is prematurely aborted without clicking 'stop recording'.
Issues during file transfer of raw .isxd files from the DAQ to the user’s computer.

Users normally discover files are corrupted when importing files into IDPS, which usually throws the following error message: Error while seeking to the beginning of JSON header at the end.

Alternatively, users can also discover files are corrupted when uploading data to IDEAS. Uploading corrupted movie files to IDEAS as a Miniscope Movie type will result in a warning appearing on the uploaded file, since IDEAS failed to read the movie for generating previews and metadata. If a warning appears after file upload, users should use this tool to try and recover the corrupted files. Refer to upload data for more details.

Description¶

This tool extracts frame data from the raw .isxd movie and writes it to a new output .isxd movie. The frame data is copied according to the the values of Width and Height configured in the input parameters. These values indicate the size of each frame in bytes to copy from the input corrupted file to the output movie. The output movie is initialized with basic timing and spacing metadata according to the input parameters.

Spacing Metadata

In order for successful recovery of frame data, users must ensure the values of Width and Height in the input parameters are set correctly based on the resolution configured in IDAS for acquisition. If these values are not set successfully, the tool will not be able to properly read and copy frame data from the corrupted file to the output file.

Timing Metadata

In addition to setting a correct resolution, users should also ensure the Start Time and Sampling Rate in the input parameters are configured correctly. These two parameters configure the timing metadata to set for the output .isxd movie. These are important timing properties often used in downstream analysis on IDEAS for synchronization & alignment with other data sets. Therefore, it's important these values are accurate according to the input movie.

Frame Metadata

This tool does not recover per-frame metadata stored in the corrupted file. It can only recover the frame data. Per-frame metadata can be important for certain operations such as de-interleaving multi-plane or multi-color movies. Therefore, users should consider the effect of losing per-frame metadata in their downstream analysis before using this tool.

Session Metadata

This tool does not recover any session metadata written by IDAS to the corrupted file.

Outputs¶

Movie¶

The output of this tool is an .isxd movie storing the recovered frames, and the timing metadata from the input parameters. This movie can be used in downstream processing tools for ISXD movies. Refer to the core workflow section for a list of compatible tools on IDEAS.

The movie will have an mp4 preview visualizing a compressed version of the extracted data.

Troubleshooting¶

I tried recovering my file but the output movie frames don't look correctly recovered
- Recovery can fail to properly extract frame data from a corrupted file if the Width and Height in the input parameters are set incorrectly based on the resolution configured in IDAS for acquisition. If these values are not set successfully, the tool will not be able to properly read and copy frame data from the corrupted file to the output file. Double check these parameter values and ensure they algin with the acquisition settings used for the input file.
I recovered my file, but I can't de-interleave the output movie using the Preprocess tool
- This tool does not recover per-frame metadata stored in the corrupted file, meaning the recovered file cannot be deinterleave by the Preprocess tool. Contact support for more assistance.