Neurolucida® USERS GUIDE VERSION 10 Copyright, trademarks, and terms of use Information in this document, including URL and other Internet Web site references, is subject to change without notice. Complying with all applicable copyright laws is the responsibility of the user. Without limiting the rights under copyright, no part of this document may be reproduced, stored in or introduced into a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, or otherwise), or for any purpose, without the express written permission of MBF Bioscience. MBF Bioscience may have patents, patent applications, trademarks, copyrights, or other intellectual property rights covering subject matter in this document. Except as expressly provided in any written license agreement from MBF Bioscience, the furnishing of this document does not give you any license to these patents, trademarks, copyrights, or other intellectual property. MicroBrightField, MBF Bioscience, Stereo Investigator, Neurolucida, Microlucida, and Neurolucida Explorer are trademarks or registered trademarks of MicroBrightField, Inc. ©1987-2011 MicroBrightField, Inc. All rights reserved. This software is based in part on the work of the Independent JPEG Group. Parts of the software are copyright © 1988-1997 Sam Leffler and copyright © 1991-1997 Silicon Graphics, Inc. All other company or product names are either trademarks or registered trademarks of their respective owners. Written and designed at MBF Bioscience (MicroBrightField, Inc.), 185 Allen Brook Lane, Suite 101, Williston, Vermont 05495 USA For any questions or problems with this software, please contact us: MBF Bioscience (MicroBrightField, Inc.) 185 Allen Brook Lane, Suite 101 Williston, Vermont 05495 USA Tel: +1-802-288-9290 Fax: +1-802-288-9002 email: [email protected] For documentation questions or suggestions, please send email to: [email protected] Visit us at: www.mbfbioscience.com Release date: 2011 March 16 Table of Contents Introducing Neurolucida 10 ............................................................................ 1 What Is Neurolucida? .............................................................................. 1 What's New In Version 10? ..................................................................... 2 Getting Help ........................................................................................... 5 Get Help from MBF Bioscience Support ................................................. 7 Training And Other Resources ................................................................ 8 Activating Your Software ............................................................................... 11 User Profiles and multiple users ............................................................. 12 Setting up the Workspace .............................................................................. 15 The Neurolucida Window, Toolbars, And Interface .............................. 15 Informational Windows And Docking Markers ..................................... 16 Setting Up My Workspace ..................................................................... 19 Hardware Considerations ....................................................................... 20 Working with Lenses ..................................................................................... 23 Lenses: Installing And Calibrating .......................................................... 23 Defining And Calibrating A New Lens .................................................. 25 Types Of Calibration ............................................................................. 31 Lucivid And Video Monitor Issues ......................................................... 33 Parcentric And Parfocal Calibration ....................................................... 35 Focus (Z-Step) Calibration .................................................................... 38 Grid Tune Current Lens ........................................................................ 41 Moving Around in Neurolucida .................................................................... 45 Using The Joystick ................................................................................. 45 Aligning The Tracing And Specimen ..................................................... 47 Moving Imported Images ....................................................................... 49 Working With AutoMove ...................................................................... 49 Working With Meander Scan ................................................................ 50 Contours and Tracing ................................................................................... 53 Tracing Contours .................................................................................. 53 Automatic Contouring ........................................................................... 54 Contour Measurements ......................................................................... 58 Editing Mode ................................................................................................ 65 Enter And Exit Edit Mode ..................................................................... 65 Selecting And Acting On Objects .......................................................... 66 i Hidden Objects ..................................................................................... 68 Editing Contours And Points ................................................................ 68 Editing Markers ..................................................................................... 74 Markers ......................................................................................................... 79 Marker Properties .................................................................................. 79 Combination Markers ........................................................................... 81 Neuron Tracing and Editing ......................................................................... 85 Tissue Preparation And Set Up .............................................................. 85 Neuron Tracing In Single Sections ........................................................ 87 Placing Markers ..................................................................................... 91 Tracing Trees In Serial Sections ............................................................. 93 Splicing ............................................................................................... 100 Tracing the Cell Body ......................................................................... 103 Editing Neuron Tracings ..................................................................... 104 Working with Upside Down Tracings ................................................. 107 Branch Order and Alternate Branch Order .......................................... 110 Creating Object Sets ............................................................................ 115 Open Delineations .............................................................................. 115 Automatic Tracing with AutoNeuron ......................................................... 119 The AutoNeuron Workflow Manager ................................................. 121 AutoNeuron Batch Run Workflow Manager ....................................... 131 Automating Your Acquires .......................................................................... 135 Automating Your Work ....................................................................... 135 The Image Stack Module ............................................................................ 143 Image stacks and lenses ........................................................................ 147 Image order and nomenclature ............................................................ 147 Viewing image stacks ........................................................................... 148 Multiple adjacent image stacks ............................................................ 148 Saving image stacks .............................................................................. 150 Tracing from image stacks ................................................................... 150 The Serial Section Manager ......................................................................... 151 The Coordinate System ....................................................................... 152 Preparing Tissues for Serial Section Reconstruction ............................. 153 The Serial Section Manager Dialog Box ............................................... 154 Setting Up The Serial Section Manager And Tracing ........................... 156 Tracing Serial Sections ......................................................................... 158 Aligning Serial Sections ....................................................................... 159 ii Serial Sections And Imported Images ................................................... 161 Using A Data Tablet With Serial Sections ............................................ 162 Working With Serial Sections—Upside Down Mountings .................. 163 The MRI Module ........................................................................................ 167 How do I load and view MRI images? .................................................. 167 The Deconvolution Module ........................................................................ 169 What