bbarad

## Convert all mitochondria STL files in current directory to SFF/HFF files
## Usage: python stl2sff.py FOLDERNAME
## Assumes there are multiple mitochondria per tomogram and up to one ER per tomogram.
## Performs both per-segment and global annotations based on assumption of MitoGFP MEF cells treated with thapsigargin (sometimes)
## Outputs HFF format sff files.
## Author: Benjamin Barad <[email protected]> with guidance from Paul Korir

import os
import sys
import glob

bbarad

# Take two binary segmentations in mrc format and combine them, with the first segmentation having label 1 and the second segmentation having label 2.

import mrcfile
import numpy as np
import argparse

def combine_segmentations(seg1, seg2, clear_overlaps=True):
    """
    Combine two binary segmentations into one, with the first segmentation having label 1 and the second segmentation having label 2.

bbarad

## Segmentation values and names are hardcoded (line 7). 
## All segmentations should be in a single "segmentations" folder.
## This should match what is used in the config.yml for surface morphometrics
from sys import argv
import mrcfile
import os
import numpy as np

component_values = {"vesicle":1,
                    "er":2,