suite2p binary conversion¶
This tool uses 2.0 compute credits per hour.
Overview¶
This suite2p binary conversion tool is a wrapper for the suite2p functions io.ome_to_binary(), io.isxd_to_binary(), and io.tiff_to_binary().
These 3 functions are called in run_s2p().
You can find more information on this processing step in the suite2p docs.
suite2p binary conversion converts the input movie(s) into a single suite2p binary file (BinaryRWFile class, namely).
Note that this tool constitutes the first step of Run suite2p pipeline.
Input files¶
| Source Parameter | File Type | File Format |
|---|---|---|
| Raw Movie Files | miniscope_movie, bruker2p_movie, image | isxd, zip, tiff |
Parameters¶
| Parameter | suite2p name | Required? | Default | Description |
|---|---|---|---|---|
| Raw Movie Files | - | True | N/A | Input 2P movie(s) [.isxd, .zip, .tiff] |
| Number of Planes | nplanes | False | 1 | [from suite2p docs] "Each tiff has this many planes in sequence." [int, =1] |
| Number of Channels | nchannels | False | 1 | [from suite2p docs] "Each tiff has this many channels per plane." [int, =1] |
| Functional Channel | functional_chan | False | 1 | [from suite2p docs] "This channel is used to extract functional ROIs (1-based, so 1 means first channel, and 2 means second channel)." [int, =1] |
| Sampling Rate | fs | False | N/A | [from suite2p docs] "Sampling rate (per plane). For instance, if you have a 10 plane recording acquired at 30Hz, then the sampling rate per plane is 3Hz, so set ops['fs'] = 3." If None (default), fs is automatically detected for Inscopix .isxd and Bruker 2P .zip files, and set to 10 Hz (suite2p default) for .tiff files. [float, 0] |
| Bruker Bidirectional | bruker_bidirectional | False | False | [from suite2p docs] "Specifies whether BRUKER files are bidirectional multiplane recordings. The True setting corresponds to the following plane order (first plane is indexed as zero): [0,1,2,2,1,0]. False corresponds to [0,1,2,0,1,2]." [bool] |
Output files¶
| File name | File type | Notes |
|---|---|---|
| data_raw.bin | suite2p binary movie | This converted binary is an instance of the suite2p BinaryRWFile class. |
| ops_binary_conversion.npy | NumPy file | Contains a dictionary of parameters populated by suite2p binary conversion. |
You can explore 1 preview movie for data_raw.bin.
You can find below an example of this preview obtained from processing a 5-minute 2P movie of mouse cortex (data courtesy of Dr. Ahmet Arac, MD, at UCLA):