Download AGScan USERS MANUAL

February 2006 Edition
INDEX
I. INTRODUCTION ..............................................................................................................................................4
I.1. A BIT OF HISTORY...............................................................................................................................................4
I.2. MAIN FEATURES OF AGSCAN...............................................................................................................................4
I.3. VOCABULARY.....................................................................................................................................................4
II. GENERAL OVERVIEW...................................................................................................................................6
II.1. THE PROCESS ....................................................................................................................................................6
II.2. FILE FORMATS...................................................................................................................................................7
II.3. IMAGE QUALITY.................................................................................................................................................7
II.4. INSTALLING AGSCAN ON YOUR COMPUTER...........................................................................................................8
II.4.a. Download...............................................................................................................................................8
II.4.b. packages contents................................................................................................................................10
II.4.c. Launching AGScan...............................................................................................................................10
III. PROCESSING STEPS ..................................................................................................................................11
III.1. USER INTERFACE ...........................................................................................................................................11
III.2. LOADING AN IMAGE FILE .................................................................................................................................12
III.3. CREATING A GRID...........................................................................................................................................16
III.4. ALIGNING A GRID ON AN IMAGE........................................................................................................................18
III.4.a. Loading a grid....................................................................................................................................18
III.4.b. aligning manually a grid....................................................................................................................19
III.4.c. Global alignment algorithm...............................................................................................................21
III.4.d. Local alignment algorithm.................................................................................................................23
III.4.e. Spot detection......................................................................................................................................26
III.5. THE TABLE ...................................................................................................................................................26
III.6. QUANTIFYING AN ALIGNMENT ..........................................................................................................................27
III.6.a. quantifications....................................................................................................................................27
III.6.b. analyze your results............................................................................................................................29
III.6.c. Export results......................................................................................................................................31
III.7. PROCESSING A BATCH......................................................................................................................................32
III.7.a. Batch tab.............................................................................................................................................32
III.7.b. Preparing the batch............................................................................................................................33
III.7.c.Save/Open a batch...............................................................................................................................36
IV. PLUGINS.........................................................................................................................................................37
IV.1. PRESENTATION...............................................................................................................................................37
IV.2. EXAMPLE: THE “MEMORY PLUGIN”..................................................................................................................37
V. FREQUENTLY ASKED QUESTIONS.........................................................................................................39
VI. INDEX..............................................................................................................................................................40
VI.1. WORD INDEX ................................................................................................................................................40
VI.2. ILLUSTRATION INDEX.......................................................................................................................................42
VII. GNU GENERAL PUBLIC LICENSE.........................................................................................................44
AGScan v0.1 User Manual
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