UPenn Cell & Developmental Biology

Core Documents

This page will be updated periodically to provide links to documents and web sites intended to help Core users with specific tasks. If you have suggestions for things you think others might find useful, please send them to Andrea Stout.

Instructions for the web calendar, phpScheduleIt (PDF file)

Sample Preparation

Counterstaining with TO-PRO-3 (for Leica confocal)

Image Acquisition

Leica document on how to set up a sequential scan (PDF file)

Zeiss "guided tour" of LSM 510 software (PDF file that launches as a slide show; although it pertains to the Meta system, much of this is also relevant to our non-Meta LSM 510)

Image Processing

MBF ImageJ Manual: If you're working with ImageJ, bookmark the McMaster Biophotonics Facility online help in your web browser. This site also has a handy collection of very useful plugins for ImageJ.

Simple ImageJ Tips: For those just getting started with ImageJ, this list of basic, commonly-used functions will get you started. (PDF file)

Quantitative Analysis

Color Measurement: This document describes an ImageJ-based procedure for measuring the areas of different colored regions in stained tissue sections imaged under brightfield illumination. (PDF file)

Guide to colocalization analysis using Metamorph Offline. You may also need these notes on how to prepare your images for colocalization analysis (both are PDF files).

MBF guide to colocalization analysis using ImageJ (formerly the WCIF guide).