MindaGap

Takes a single panorama image and fills the empty grid lines with neighbour-weighted values. Small box sizes yield limited results but work the best with a high loop number (like 40). Increase boxsize to overcome bigger gaps.

Ricardo Guerreiro, Resolve Biosciences GmbH

INSTALLATION

• You need a terminal and Python installed. If you don’t, do the following:

  • I recommend the git bash terminal. Download and install it.
  • Right click on any folder you want to work on. A new option exists “Git Bash here”, click there. A bash terminal is open.
  • Type python and enter. An automatic windows prompt allows you to install it.
  • Enter this in the bash terminal: echo "alias python=' winpty python.exe'" >> ~/.bashrc ; source ~/.bashrc

• To install the python dependencies, enter the following on the terminal:

pip3 install tifffile opencv-python

• Install MindaGap:

cd ; mkdir Programs; cd Programs
git clone https://github.com/ViriatoII/MindaGap/

USAGE

Open git bash terminal on your desired directory and run:
python ~/Programs/MindaGap/mindagap.py INPUT_PANORAMA.tif [BOXSIZE] [LOOPNUM] [--edges True/False]

  Optional parameters:
  BOXSIZE Default 3. A larger number allows to overcome large gaps, but makes looses fine details in new filled grid.      
  LOOPNUM Default 40. A smaller number is faster, but the result is less good.       
  --edges Default False. An optional parameter to blur area around grid, for smoother transitions between tiles with different exposures (EXPERIMENTAL).   

Additional scripts

Create RGB composite panorama from gapfilled images

python ~/Programs/MindaGap/rgb_from_z_tiles.py -b DAPI.tiff -r red_channel.tiff -g constructive_green_channel.tiff

Mark duplicate reads along gridline edges

python ~/Programs/MindaGap/duplicate_finder.py XYZ_coordinates.csv [Xtilesize] [Ytilesize] [windowsize] [maxfreq] [minMode] [-p True/False]

Docker

To use MindaGap with Docker, you can pull the prebuild docker image from Dockerhub or follow the steps below to build the Docker image.

You can then execute the script using a docker container with all required dependencies available:

## Pull the prebuild docker image from Docker hub
docker pull rguerr/mindagap:latest

#### To build the docker image yourself
## Clone this git repository
git clone https://github.com/ViriatoII/MindaGap.git
cd MindaGap

## Build docker image
docker build -t mindagap .

## Test that docker build worked successfully
docker run --rm -it mindagap:latest \
python /mindagap/mindagap.py

How to cite

  Ricardo Guerreiro, Florian Wuennemann, & pvtodorov. (2023). ViriatoII/MindaGap: v0.0.3 (0.0.3). Zenodo. https://doi.org/10.5281/zenodo.8120559