jmuhlich

# requires libtiff command line tools to be installed (tiffinfo/tiffset)
# this is only intended to be run on SVS files from Versa scanners which display as bright pink
# ideally this should be run before importing to OMERO

# the recommended pre-import workflow is:
#   1. Make sure Bio-Formats command line tools are available.
#      See https://docs.openmicroscopy.org/bio-formats/latest/users/comlinetools/index.html
#   2. Use "showinf -crop 0,0,512,512" on the SVS file to verify that it is bright pink.
#   3. Back up the SVS file.
#   4. Run this script to update the file in-place ("./svs-fix-colors.sh /path/to/file.svs").

jmuhlich

from ashlar.fileseries import FileSeriesReader
from ashlar.reg import EdgeAligner, Mosaic, PyramidWriter
import numpy as np
import pandas as pd
import skimage.exposure, skimage.filters, skimage.io
import sys
import tifffile

input_tif_path = sys.argv[1]
pattern = "20231124_203726_S1_C902_P99_N99_F{series}.TIF"

jmuhlich

params {
    config_profile_description = 'HMS O2 profile.'
    config_profile_contact = 'Jeremy Muhlich'
    config_profile_url = 'https://...'
    singularity_cache_dir = '/n/groups/lsp/mcmicro/singularity'
}

process {
    executor = "slurm"
    queue = { task.time < 12.h ? 'short' : task.time < 5.d ? 'medium' : 'long' }

jmuhlich

import argparse
from ashlar.reg import EdgeAligner, Mosaic, PyramidWriter
from ashlar.scripts.ashlar import build_reader, HelpFormatter
import networkx as nx

parser = argparse.ArgumentParser(
    description='Stitch one multi-tile image with strict stage path following',
    formatter_class=HelpFormatter,
)
parser.add_argument(

jmuhlich

import argparse
from ashlar import reg, transform
import ashlar.scripts.ashlar as ascript
from magicgui import magicgui
import napari
import numpy as np
import skimage
import sys
from typing import List

jmuhlich

import bibtexparser
from pylatexenc.latex2text import LatexNodes2Text
import sys
import yaml

lt = LatexNodes2Text()

with open(sys.argv[1]) as f:
    db = bibtexparser.load(f)
for e in db.entries:

jmuhlich

# usage: ome-tiff-set-resolution.py [-h] image size
#
# Set physical pixel dimensions in an OME-TIFF
#
# positional arguments:
#   image       OME-TIFF file to modify
#   size        pixel width in microns
#
# optional arguments:
#   -h, --help  show this help message and exit

jmuhlich

import sys
import re
import importlib
import time
from pysb.simulator import ScipyOdeSimulator
import pysb.bng
import numpy as np


def benchmark(model, sim_kwargs):

jmuhlich

#!/bin/bash

echo "start"
for ((i=1; i<=32000; i++)); do
    echo "STDERR $i" >&2
done
echo "normal 1"
sleep 1
for ((i=1; i<=32000; i++)); do
    echo "STDERR $i" >&2

jmuhlich

import sys
import io
import warnings
import xml.etree.ElementTree
import tifffile

if len(sys.argv) != 2:
    print(f"Usage: ometiff-channel-names.py input.ome.tif")
    print("Print the channel names for the first image in an OME-TIFF file.")
    sys.exit(1)