This repository contains Python scripts and ImageJ macros that were used in the analysis of Drosophila phenotype screens done for the following puplication:
"Functional unknomics: Systematic screening of conserved genes of unknown function" Joao Rocha, Satish Arcot Jayaram, Tim J Stevens, Nadine Muschalik, Rajen D Shah, Sahar Emran, Cristina Robles, Matthew Freeman, Sean Munro PLoS Biol. 2023 Aug; 21(8): e3002222 PMID: 37552676
If you are looking for scripts relating to the setup of the Unknome Database, which underpins the Unknome web site please see the unknome_db repository.
Contains functions for the setup of FlyWheel images; detection of plate edges, wells, image alignment etc.
Performs the ECC transform, using OpenCV, to align flywheel images with their first, reference frame.
Takes a plate image and extracts contours corresponding to wells. Returns a list of the coordinates of the centres of the contours and a resized image whose histogram was equalised.
Takes well centre coordinates, clusters them in rows and fits linear regression lines to clusters to returns a sequence of line fits for the rows.
Takes a sequence of the plat rows linefits and returns the row and column bestfits. Also outputs intersects of the best-fits at the edges and centre of the plate image.
Takes a plate image and a list object containing m and b parameters of row and column bestfits and respective intersect datapoints at the edges and centre of the image. Returns a list object containing the coordinates of the homography vertices of the plate; homography vertices: H12, H1, A12 and A1 well's centres. Also returns the location of the row and column bestfits
Estimate well positions and plate corners from homography vertices.
Contains functions to analyse the FlyWheel images to track fly motion. Plotting functions for the derived tracking data.
Tracks flies in plate images using intensity contours after background subtration.
Estimates time of death within plate wells; when movement consistently ceases.