Fiji使用手册_Fiji打不开图片资源-CSDN文库

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Contents

About this Manual .................................................................................................................................. 1

Introduction ........................................................................................................................................ 1

A Note on Image Analysis ................................................................................................................... 1

Distribution ......................................................................................................................................... 1

Authors ................................................................................................................................................ 2

Requirements ...................................................................................................................................... 2

Initial Setup ......................................................................................................................................... 2

Image Contributors ............................................................................................................................. 4

Introduction to Fiji .................................................................................................................................. 5

Introduction ........................................................................................................................................ 5

Where to get Fiji ................................................................................................................................. 5

Configuration ...................................................................................................................................... 6

Memory and Processor Threads ..................................................................................................... 6

Proxy Settings .................................................................................................................................. 8

Updates ........................................................................................................................................... 9

Monitoring and Clearing up Excess Memory Usage ......................................................................... 11

Monitoring Memory ..................................................................................................................... 11

Basic Module ......................................................................................................................................... 13

Basic Navigation in Fiji .......................................................................................................................... 14

Aim .................................................................................................................................................... 14

Opening Files ..................................................................................................................................... 14

Zooming In and Out .......................................................................................................................... 15

Panning the Image ............................................................................................................................ 15

Duplicating an Image ........................................................................................................................ 16

Regions of Interest (ROI) ................................................................................................................... 17

Drawing ROIs ................................................................................................................................. 17

Moving ROIs .................................................................................................................................. 18

Resizing ROIs ................................................................................................................................. 18

Using the ROI Manager to add Multiple ROIs ............................................................................... 18

Adjusting Brightness and Contrast ........................................................................................................ 20

Aim .................................................................................................................................................... 20

Adjusting Brightness and Contrast – Colour Images ......................................................................... 20

Adjusting the Colour Balance – Colour Images ................................................................................. 22

Adjusting the Brightness and Contrast – Monochrome Images ....................................................... 24

Calibrating and Adding a Scale Bar ....................................................................................................... 27

Aim .................................................................................................................................................... 27

Calibrating an Image ......................................................................................................................... 27

Adding a Scale Bar ............................................................................................................................. 29

Fluorescent Images – Changing Bit Depth, Adding Colour, Merging Images and Simulating Colour

Blindness ............................................................................................................................................... 30

Aim .................................................................................................................................................... 30

Changing Bit Depth – 24bit RGB ....................................................................................................... 31

Adding Colour – Using Lookup Tables ............................................................................................... 32

Single Colour LUTs ......................................................................................................................... 32

Multicolour LUTs ........................................................................................................................... 33

Intensity Distribution .................................................................................................................... 34

Merging Images ................................................................................................................................ 36

Merging Up To 7 Channels and DIC/Phase/Brightfield – Standard Colours ................................. 36

Merging Up To 7 Channels and DIC/Phase/Brightfield – Non-standard Colours ......................... 38

Merging 8 or more colour channels .............................................................................................. 41

Simulating Colour Blindness ............................................................................................................. 44

Opening Confocal and Deconvolution Data Sets .................................................................................. 46

Aim .................................................................................................................................................... 46

LOCI Tools ......................................................................................................................................... 46

Initial File Opening ........................................................................................................................ 46

Displaying Metadata ..................................................................................................................... 47

Default Opening States ................................................................................................................. 47

Opening Confocal Data ..................................................................................................................... 49

Leica – LIF Format ......................................................................................................................... 49

Nikon – ICS/IDS File Format .......................................................................................................... 54

Nikon – ND2 File Format ............................................................................................................... 56

Olympus – OIB and OIF File Format .............................................................................................. 60

Zeiss – LSM File Format ................................................................................................................. 62

Opening DeltaVision Data ................................................................................................................. 63

Visualising 3D and Live Data ................................................................................................................. 65

Aim .................................................................................................................................................... 65

Visualising 3D Data............................................................................................................................ 65

Z Projection ................................................................................................................................... 65

Orthogonal Projection................................................................................................................... 67

Slice Montage................................................................................................................................ 68

3D Volume – Simple ...................................................................................................................... 70

Making Movies .................................................................................................................................. 72

Simple Analysis – Area and Intensity of Stain ....................................................................................... 74

Aim .................................................................................................................................................... 74

Measuring the Area and Intensity of Stain - Fluorescence ............................................................... 74

Separating Merged Multichannel Images ..................................................................................... 74

Threshold Image ........................................................................................................................... 75

Automatic Threshold Algorithms .................................................................................................. 77

Measure Thresholded Area........................................................................................................... 78

Measuring the Area of Stain – Brightfield......................................................................................... 81

Make a Brightfield Image Look like a Fluorescent One ................................................................ 83

Cell Counting ......................................................................................................................................... 85

Aim .................................................................................................................................................... 85

Initial Binary Creation ....................................................................................................................... 85

Counting Cells – Basic Count ............................................................................................................. 88

Counting Cells – Detailed Information .............................................................................................. 91

Cell Segmentation and Analysis ............................................................................................................ 95

Aim .................................................................................................................................................... 95

Creating Whole Cell Binary Masks .................................................................................................... 95

Analysing the Image ........................................................................................................................ 103

Checking the Effectiveness of Segmentation .................................................................................. 105

Method 1 – ROI Manager ........................................................................................................... 105