Skip to content

Instantly share code, notes, and snippets.

Avatar

André F. Rendeiro afrendeiro

View GitHub Profile
@afrendeiro
afrendeiro / markers_to_cell_type_labels.yaml
Last active Sep 21, 2021
Annotation of marker epitopes for various cell types
View markers_to_cell_type_labels.yaml
# 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
afrendeiro / mask_to_labelme_json.py
Created Jul 7, 2021
Convert a labeled image mask to a JSON file compatible with labelme. Useful to export predictions and then fine tune by hand with labelme.
View mask_to_labelme_json.py
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,
View triangular_clustermap.py
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
afrendeiro / interactive_volume_viewer.py
Created May 21, 2021
An example program to display a volumetric image from the command line using matplotlib
View interactive_volume_viewer.py
#!/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
@afrendeiro
afrendeiro / upload_zipfiles_to_box.py
Created Feb 1, 2021
Upload content of zipfiles to box.com programmatically
View upload_zipfiles_to_box.py
#!/usr/bin/env python
"""
Upload images inside zip files to box.com.
"""
import sys, time, webbrowser, json, zipfile, tempfile, urllib3
from argparse import ArgumentParser
from pathlib import Path
from typing import Dict, List, Generator
@afrendeiro
afrendeiro / dog_ex.py
Created Dec 29, 2020 — forked from leonidk/dog_ex.py
difference of gaussians example in python
View dog_ex.py
from skimage import data, feature, color, filters, img_as_float
from matplotlib import pyplot as plt
original_image = img_as_float(data.chelsea())
img = color.rgb2gray(original_image)
k = 1.6
plt.subplot(2,3,1)
@afrendeiro
afrendeiro / nih_grant_link_eracommons.md
Last active Dec 28, 2020
Linking NIH grant number to publications in NCBI/eRA Commons
View nih_grant_link_eracommons.md
@afrendeiro
afrendeiro / series_matrix2csv.py
Created Dec 10, 2020
Get a GEO series matrix file describing an experiment and parse it into project level and sample level data.
View series_matrix2csv.py
#!/usr/bin/env python
"""
Get a GEO series matrix file describing an experiment and
parse it into project level and sample level data.
"""
import os
from typing import Tuple, Union
import tempfile
@afrendeiro
afrendeiro / get_gene_set_libraries.py
Last active Nov 30, 2020
Download gene set libraries from Enrichr in GMT format for ssGSEA - done in parallel with async
View get_gene_set_libraries.py
from pathlib import Path
import parmap
import requests
def update(gsll):
return [g for g in gsll if not (output_dir / (g + ".gmt")).exists()]
@afrendeiro
afrendeiro / stitching_demo.py
Created Sep 14, 2020
Reduce and stitch Operetta microscope images
View stitching_demo.py
#!/usr/bin/env python
"""
Max-reduce and stitch microscopy images into one stitched one.
Requirements:
`pip install numpy matplotlib tifffile`
"""
from pathlib import Path