MEOW : Membrane Eraser for Optimized Workflow

MEOW is a wrapper that aims at eraising membranes from your tomography data in order to make your life easier

It is based on membrain-seg to automoatically segment the membranes on your subvolumes and fidder to replace the membranes with noise.

It comes in two flavours:

• MEOW_3d is intended to be used inside the Dynamo workflow to erase out the membranes for your already exracted subvolumes for easier alignment of your particles !
• MEOW_2d is erasing the membranes from the tilt series (based on the same idea as fiducials for fidder) for all the pipelines that do not work with subvolumes anymore (or any other usage)

Installation

MEOW_3d

Please install eveything that you need inside a conda environnement

conda create -n MEOW python=3.10
conda activate MEOW
pip install membrain-seg cryohub
pip install git+https://github.com/brisvag/fidder@feature/3d
pip install torch_cubic_spline_grids

Please install if you don't already have it GNU parallel

sudo apt install parallel

You will also need to have the Membrain-seg checkpoint in your working directory. You can download the latest version here

MEOW_2d

work in progress...

Basic Usage

MEOW_3d

From the command line, using 32 CPUs and expanding the mask by 5 pixels in all directions

./MEOW_3d.sh directory_where_the_subvolumes_are/ 32 5

MEOW will create a subtomos_erased/ directory with your particles without a membrane, the particle number is kept so you can directly use the table file you aready have for alignments!!

MEOW_2d

./MEOW_2d.sh directory_where_the_tomograms_are/ where_the_tilt_series_are/ tilt_file.tlt