Convert Bruker 2P Data To ISXD Movie¶
This tool uses 0.5 compute credits per hour.
This tool converts Bruker 2P movie data to the .isxd format, enabling downstream analysis with other IDEAS tools.
Inputs¶
| Parameter | Required? | Default | Description |
|---|---|---|---|
| Compressed Files | True | N/A | Compressed files containing Bruker 2P data. Supported file formats are: .zip. Currently only single file inputs are accepted. |
| Temporal Downsampling Factor | True | 1 | Temporal downsamping factor to apply on frames before writing to isxd movie. |
| Spatial Downsampling Factor | True | 1 | Spatial downsampling factor to apply on frames before writing to isxd movie. |
| Crop Rectangle | False | N/A | Draw a crop rectangle to apply on frames before writing to isxd movie. |
File Inputs¶
| Source Parameter | File Type | File Format |
|---|---|---|
| Compressed Files | bruker2p_movie | zip |
Bruker 2P Data¶
The tool expects a compressed .zip file, containing the following files:
- At least one
.tifor.tifffile containing the frame data of the Bruker 2P movie.- If there is one file, then the tool assumes the file is a multi-stack tiff consisting of multiple frames
- If there are multiple files, then the tool assumes each file is a single frame tiff, and the files are named in chronological order.
- One
.xmlfile containing metadata about the Bruker 2P movie including frame timestamps, and microscope & session settings
Description¶
This tool extracts the contents of the input compressed data. It checks that there is at least one .tif or .tiff file and one .xml file in the archive.
If there is one tiff file, then the tool assumes the file is a multi-stack tiff with multiple frames.
The tool reads one frame of the multi-stack tiff at a time, and writes to an .isxd file.
If there are multiple tiff files, then the tool assumes each file is a single frame tiff, and the files are named in chronological order.
The tool reads one tiff file at a time, and writes to an .isxd file.
Before writing a frame to the .isxd file, the tool will apply spatial downsampling on the frame if a value greater than one is specified.
If temporal dowsampling is applied, the frame is only written if the frame number is a multiple of the temporal downsampling factor.
The tool also extracts the following timing metadata from the .xml file:
- The start time of the recording, read from the
dateattribute of the file - The average frame period. This is calculated by reading frame timestamps from the
relativeTimekey inSequence/Frameelements of the file. The time difference between consecutive frames is averaged.
The .isxd movie is configured with these timing settings, enabling appropriate playback and accurate alignment with other datasets.
Outputs¶
Movie¶
The output of this tool is an .isxd movie storing the tiff frames, and the timing metadata from the .xml, extracted from the Bruker 2P movie.
This movie can be used in downstream processing tools such as:
The movie will have an mp4 preview visualizing a compressed version of the extracted data.
