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paul-english / pathvisions24.bib
Created November 7, 2024 20:24
Some bookmarks & research saved from PathVisions 2024
@misc{kalra_yottixel_2019,
title = {Yottixel -- {An} {Image} {Search} {Engine} for {Large} {Archives} of {Histopathology} {Whole} {Slide} {Images}},
url = {http://arxiv.org/abs/1911.08748},
doi = {10.48550/arXiv.1911.08748},
abstract = {With the emergence of digital pathology, searching for similar images in large archives has gained considerable attention. Image retrieval can provide pathologists with unprecedented access to the evidence embodied in already diagnosed and treated cases from the past. This paper proposes a search engine specialized for digital pathology, called Yottixel, a portmanteau for "one yotta pixel," alluding to the big-data nature of histopathology images. The most impressive characteristic of Yottixel is its ability to represent whole slide images (WSIs) in a compact manner. Yottixel can perform millions of searches in real-time with a high search accuracy and low storage profile. Yottixel uses an intelligent indexing algorithm capable of representing WSIs with a mosaic of patches
#!/usr/bin/env python3
import json
import functools
import ollama
from pydantic import BaseModel, create_model
from inspect import signature
from typing_utils import issubtype
from jsf import JSF
import os
import sqlite3
from xml.etree.ElementTree import iterparse
from tqdm import tqdm
import json
def create_database(dbname: str):
# Create a connection to the SQLite database
conn = sqlite3.connect(dbname)
### version information
```
pre-commit version: 2.18.1
git --version: git version 2.32.0 (Apple Git-132)
sys.version:
3.9.7 (default, Sep 16 2021, 08:50:36)
[Clang 10.0.0 ]
sys.executable: /Users//opt/anaconda3/bin/python
os.name: posix
@paul-english
paul-english / keybase.md
Created March 17, 2022 17:48
keybase.md

Keybase proof

I hereby claim:

  • I am paul-english on github.
  • I am log0ymxm (https://keybase.io/log0ymxm) on keybase.
  • I have a public key whose fingerprint is 09EA 4D46 DD08 D8E3 CEC3 AA7C A967 2C1A 03D1 840A

To claim this, I am signing this object:

<!DOCTYPE html>
<head>
<meta http-equiv="content-type" content="text/html; charset=UTF-8" />
<script>
L_NO_TOUCH = false;
L_DISABLE_3D = false;
</script>
<style>html, body {width: 100%;height: 100%;margin: 0;padding: 0;}</style>
@paul-english
paul-english / unisplat.py
Created August 16, 2021 19:25
Convert uniprot_trembl to massive csv
from tqdm import tqdm
import csv
order = [
"",
"ID",
"AC",
"DT",
"DE",
"GN",
@paul-english
paul-english / redis_disjoint_set.py
Created December 27, 2019 19:17
Redis Disjoint Set
import random
class RedisDisjointSet(object):
"""
https://en.wikipedia.org/wiki/Disjoint-set_data_structure
UTF-8 based persistent disjoint set structure that just assumes there's a local redis
"""
def __init__(self, seed=None):
@paul-english
paul-english / gist:f1f9527fdeed923ce11c70e4713d3c62
Created September 4, 2019 22:09
unlocked screen one liner
echo "echo 'sleep 1' >> ~/.profile" >> ~/.profile
create table penglish_scratch.naics_desc_lookup (
code varchar(6) sortkey distkey,
description varchar(255)
);
insert into penglish_scratch.naics_desc_lookup values
('11', 'Agriculture, Forestry, Fishing and Hunting'),
('111', 'Crop Production'),
('1111', 'Oilseed and Grain Farming'),