fish-reg 0.0.2

fish video registration software

# fish_reg

Simple program that uses rigid registration to stabilise video of zebrafish under electrophysiology microscope.

## Setup ` pip install fish_reg `

## Usage

However you use it now it will save the corrected video in the same directory as the original video but with the suffix “_fixed”.

Basic usage ` fish_reg_execute path/to/file.tif ` Perform on directory of files ` fish_reg_execute path/to/directory -d ` define coarsness of registration (-r) and width of smoothing window (-w) ` fish_reg_execute path/to/file.tif -r 2 -w 5 ` Using only slice of video to test performance. The start (-s) and end (-e) tags are optional and determine boundries of video slice. ` fish_reg_execute path/to/file.tif -sl -s 500 -e 700 `

## Limitations - Tested on single system, might have problems with data from other sources - Only works with .tif files - Only uses rigid registration, as of yet no option for deformable registration