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@mutterer
mutterer / white_balance_from_grey_area.ijm
Created June 5, 2019 08:10
white_balance_from_grey_area corrects an RGB image white balance using a reference ROI
setBatchMode(1);
t=getTitle();
getBoundingRect(x, y, width, height);
run("Select None");
run("Duplicate..." , "title=ori duplicate");
makeRectangle(x, y, width, height);
run("RGB Stack");
run("32-bit");
id=getImageID;
run("Duplicate..." , "title=temp duplicate");
@kauffmanes
kauffmanes / install_anaconda.md
Last active June 5, 2025 21:18
Install Anaconda on Windows Subsystem for Linux (WSL)

Thanks everyone for commenting/contributing! I made this in college for a class and I no longer really use the technology. I encourage you all to help each other, but I probably won't be answering questions anymore.

This article is also on my blog: https://emilykauffman.com/blog/install-anaconda-on-wsl

Note: $ denotes the start of a command. Don't actually type this.

Steps to Install Anaconda on Windows Ubuntu Terminal

  1. Install WSL (Ubuntu for Windows - can be found in Windows Store). I recommend the latest version (I'm using 18.04) because there are some bugs they worked out during 14/16 (microsoft/WSL#785)
  2. Go to https://repo.continuum.io/archive to find the list of Anaconda releases
  3. Select the release you want. I have a 64-bit computer, so I chose the latest release ending in x86_64.sh. If I had a 32-bit computer, I'd select the x86.sh version. If you accidentally try to install the wrong one, you'll get a warning in the terminal. I chose `Anaconda3-5.2.0-Li
@DarwinAwardWinner
DarwinAwardWinner / analyze_pkg_usage.R
Last active February 12, 2025 16:27
Script for finding loaded but unused packages in R scripts
#!/usr/bin/env Rscript
suppressPackageStartupMessages({
library(globals)
library(readr)
library(stringr)
library(rex)
library(magrittr)
library(rlang)
library(knitr)
@bmaupin
bmaupin / free-backend-hosting.md
Last active June 18, 2025 17:13
Free backend hosting
@Svidro
Svidro / !Making Measurements in QuPath
Last active October 15, 2024 06:00
Making Measurements in QuPath
Collections of scripts harvested mainly from Pete, but also picked up from the forums
TOC
Accessing dynamic measurements.groovy - Most annotation measurements are dynamically created when you click on the annotation, and
are not accessible through the standard getMeasurement function. This is a way around that.
Affine transformation.groovy - access more accurate measurements for the affine transformation used in the image alignment (m5/m6+)
Alignment of local cells.groovy - check neighborhood for similarly aligned cells
@fasiha
fasiha / DictionaryOfJapaneseGrammar.csv
Created December 15, 2017 04:39
All example sentences from Seiichi Makino and Michio Tsutsui's series of three Japanese grammar dictionaries: "Dictionary of Basic Japanese Grammar", "Intermediate" and "Advanced
We can't make this file beautiful and searchable because it's too large.
Number,Expression,Translation,Reading,Grammar Japanese,Grammar English,Grammar Explanation,Notes,Picture,Page,Level,Scrambled
1,私は良子に花をあげた・あげました。,I gave Yoshiko flowers.,私[わたし]は 良子[りょうこ]に 花[はな]をあげた・あげました。,あげる,,give | Someone gives something to a person who is not a member of the giver’s in group but whose status is about equal to that of the giver.,,,63,Basic,
2,大野さんは山本さんに本をあげた。,Ms. Ono gave Mr. Yamamoto a book.,大野[おおの]さんは 山本[やまもと]さんに 本[ほん]をあげた。,あげる,,give | Someone gives something to a person who is not a member of the giver’s in group but whose status is about equal to that of the giver.,,,63,Basic,scrambled
3,君はアンに何をあげましたか。,What did you give to Ann?,君[きみ]はアンに 何[なに]をあげましたか。,あげる,,give | Someone gives something to a person who is not a member of the giver’s in group but whose status is about equal to that of the giver.,,,63,Basic,scrambled
4,私は信男さんにネクタイを買ってあげた・あげました。,I bought a tie for Nobuo.,私[わたし]は 信男[のぶお]さんにネクタイを 買[か]ってあげた・あげました。,あげる,,do s.t. for s.o.; do s.o. a favor by doing s.t. |&nbs
@stephenturner
stephenturner / keybindings.json
Created May 31, 2017 21:04
VSCode keybindings to replicate my most commonly used RStudio shortcuts (Mac)
// Place your key bindings in this file to overwrite the defaults
[
// RStudio: Copy lines up/down with alt+cmd+up/down
{
"key": "alt+cmd+down",
"command": "editor.action.copyLinesDownAction",
"when": "editorTextFocus && !editorReadonly"
},
{
"key": "shift+alt+down",
@ipurusho
ipurusho / STAR.md
Last active June 18, 2025 22:25
A brief tutorial on how to run the STAR aligner on medinfo.mssm.edu

###Download STAR### Obtain STAR source from https://github.com/alexdobin/STAR

Add the following to your .bashrc file and source it: export PATH=/path/to/STAR/bin/:$PATH

###Generate Reference Genome

@bishboria
bishboria / springer-free-maths-books.md
Last active May 10, 2025 04:28
Springer made a bunch of books available for free, these were the direct links
@arne-cl
arne-cl / restore_packages.R
Created September 16, 2014 08:46
save/load/install a list of your currently installed R packages
# restore_packages.R
#
# installs each package from the stored list of packages
# source: http://hlplab.wordpress.com/2012/06/01/transferring-installed-packages-between-different-installations-of-r/
load("~/installed_packages.rda")
for (count in 1:length(installedpackages)) {
install.packages(installedpackages[count])
}