omsai

// Upload image from stack to SLM before each frame in MDA.
//
// We have to use the core API to upload each frame individually,
// since there is no public sequencing API for SLM devices.
//
// Pariksheet Nanda <pariksheet.nanda@uconn.edu> July 2014
//
// License: Public Domain

import ij.io.Opener; // To load TIFF stack file from disk.

omsai

// Close shutter after specified delay.
//
// In response to James' question on the mailing list:
// http://micro-manager.3463995.n2.nabble.com/Tethered-Cam-Sutter-Shutter-Closure-Delay-td7583216.html

// Set this variable to however long you need your shutter to be open.
delayBeforeShutterCloseMs = 800;

// Opens shutter and sets timer to close shutter.
Runnable synchronizedShutter = new Runnable() {

omsai

// Map time stamps to image labels.
//
// Running this script adds a timestamp label to each image slice.
// Thus the timestamp shows up in paranthesis in the info bar on top
// of the image.
//
// Adapted from planeTimings.txt in bioformats repository:
// https://github.com/openmicroscopy/bioformats/blob/v5.0.2/components/bio-formats-plugins/utils/macros/planeTimings.txt
//
// Pariksheet Nanda <omsai@member.fsf.org> 2014-06-19

omsai

@echo off

rem Copy settings from 32-bit MetaMorph to fresh 64-bit MetaMorph.
rem
rem Usage: Change the values of mm_old_folder and mm_new_folder as
rem necessary and run the script.
rem 
rem Pariksheet Nanda <p.nanda@andor.com> 2014-05-06
rem
rem License: Public Domain

omsai

// Prints time intervals from most recently selected MDA data window.
//
// Reads "ElapsedTime-ms" property from image metadata to calculate
// image intervals. Sets first frame to 0 ms.
//
// One current limitation of the MM API (and therefore this script) is
// we to the most recently selected MDA data window (it's possible the
// user most recently selected the snap window or an ImageJ image
// window), so one has to prompt the user to select an MDA data
// window.  One could add a "getActiveAcquisitionName()" to the gui

omsai

"""
Reset MetaMorph user toolbars to default value.

When migrating from 32-bit to 64-bit MetaMorph, sometimes the
mmproc.cfg files have toolbar information that causes MetaMorph to
crash on startup.  Reset these to the state found in a new mmproc.cfg
file.

Pariksheet Nanda <p.nanda@andor.com> 2014-03-27
License: Public Domain

sloria

The Best of the Best Practices (BOBP) Guide for Python

A "Best of the Best Practices" (BOBP) guide to developing in Python.

In General

Values

• "Build tools for others that you want to be built for you." - Kenneth Reitz
• "Simplicity is alway better than functionality." - Pieter Hintjens

drinks

// ==ClosureCompiler==
// @output_file_name default.js
// @compilation_level SIMPLE_OPTIMIZATIONS
// ==/ClosureCompiler==

/*

**Notes**

In some cases, forms will still get submitted when you click the submit button.

omsai

/**
 * Split Stack macro
 *
 * Fixes MetaMorph dual camera image files, by splitting them into
 * their separate channel files.
 *
 * Usage: In ImageJ, use Plugins > Macros > Run...
 *
 * Description:
 * 

omsai

#SHELL

"""
Calculate Spinning Disk uniformity and compare with Andor's specification.

Usage:
Start the Python IDE from iQ from under Plugins.  Run this Plugin from
the iQ menu and select the "Progress" tab.
Run a protocol with just "Snap" and loop protocol enabled to collect images.
The bar will update to show how close the image drop-off.