André F. Rendeiro afrendeiro

Principal Investigator at CeMM - Research Center for Molecular Medicine, Vienna Austria; Leading @rendeirolab

afrendeiro / test_nuclei_dataloaders.py

Last active November 21, 2023 17:46

Use torch dataloaders with nuclei coordinates for training.

	"""
	Use dataloaders with nuclei coordinates for training.
	"""

	from functools import partial

	import requests
	import h5py
	from tqdm import tqdm
	import numpy as np

afrendeiro / rasterize_pdf.sh

Created October 30, 2023 08:37

Rasterize PDF files

	#!/bin/bash

	# Terminate on first error
	set -e

	# Check if input file is provided
	if [ -z "$1" ]; then
	echo "Usage: $0 <input_file.pdf>"
	exit 1
	fi

afrendeiro / test_gpus_accelerate.py

Created July 24, 2023 08:11

Multi-GPU training with hf-accelerate

	#!/usr/bin/env python

	"""
	A simple example of how to use the Accelerator API
	to train a vision model on a dummy dataset.

	Accelerator enables training on a single or multiple GPUs.

	Run once `accelerate config` to set up your configuration file.

afrendeiro / quantization_experiments.py

Last active March 9, 2023 15:36

Run experiments on different quantization settings and report speedup and error.

	"""
	Run the experiments for the quantization speedup and plot results.
	"""

	import subprocess

	import numpy as np
	import pandas as pd
	import matplotlib.pyplot as plt
	import seaborn as sns

afrendeiro / fix_indica_tiff.py

Last active June 30, 2022 15:26

Read IndicaLabs TIFF files (exported from HALO) and write TIFF file.

	"""
	Convert a TIFF file generated by IndicaLabs (HALO) to a usable TIFF file.
	"""

	import typing as tp
	from pathlib import Path
	from xml.etree import ElementTree

	import tifffile
	from tifffile.tiffcomment import tiffcomment

afrendeiro / macsima_liver.py

Last active June 17, 2022 10:25

Quick look at MACSIMA data from https://cloud.irc.ugent.be/public/index.php/s/WPRWfQi6MKSF3Ex

	from pathlib import Path
	import tifffile
	import numpy as np
	import matplotlib.pyplot as plt
	from matplotlib.backends.backend_pdf import PdfPages
	from stardist.models import StarDist2D
	from csbdeep.utils import normalize

	_dir = Path("HumanLiverH35")
	files = list(

afrendeiro / markers_to_cell_type_labels.yaml

Last active May 9, 2022 14:39

Annotation of marker epitopes for various cell types

	# This annotation of cell type markers is tailored for surface proteins
	# normally profilid with multiplexed imaging (IMC, CODEX).
	# It is a simple reference for myself and may be more detailed in some parts than others.
	# This reference is hierarchical.
	# This annotation is generally pan-tissue.
	# Author: Andre Rendeiro
	# License: CC BY-SA 2.0

	cell_types:
	structural:

afrendeiro / mask_to_labelme_json.py

Created July 7, 2021 17:23

Convert a labeled image mask to a JSON file compatible with labelme. Useful to export predictions and then fine tune by hand with labelme.

	import pathlib

	import numpy as np

	def mask_to_labelme(
	labeled_image: np.ndarray,
	filename: pathlib.Path,
	overwrite: bool = False,
	simplify: bool = True,
	simplification_threshold: float = 5.0,

afrendeiro / triangular_clustermap.py

Created June 9, 2021 00:08

	import string

	import numpy as np
	import pandas as pd
	import matplotlib.pyplot as plt
	import seaborn as sns

	# generate some data
	n_groups = 4
	n_per_group = 5

afrendeiro / interactive_volume_viewer.py

Created May 21, 2021 16:58

An example program to display a volumetric image from the command line using matplotlib

	#!/usr/bin/env python

	"""
	An example program to display a volumetric image from the command line.
	"""

	import sys
	import typing as tp
	from urlpath import URL
	from functools import partial