Batch Adjusting Lookup Tables, B/C & Making Montagesbiop.epfl.ch/pdf/Common...

Batch Adjusting Lookup Tables, B/C & Making Montages

Examples using Common Tools ActionBarOlivier Burri, Romain Guiet

EPFL BIOP 2015

Common Tools ActionBar

• Install using our Update site PTBIOP

You also need ActionBar from Jerome Mutterer 1

The Interesting Bits

• LUT– Allows to apply modified LUTs to an

image or a folder of images

• B & C – Applies a specific Min & Max to each

channel on an image or a folder

• Montage– Creates a Montage from a

multichannel image or a folder of images

When Applying on a Folder, the macro creates a subfolder, and does not overwrite any data 2

Apply a LUT

1. Have a multichannel image open2. Click on "Channels LUT Selection"3. Change your LUTs4. The settings appear on a Window

called "Common Tools"5. Click on "…on the current image"

to apply6. Apply it on a folder if desired

Before After

The settings can be saved to be reused at a different time:From the Common Tools bar, click on "Save Parameters"

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Change Display Range

1. Have a multichannel image open2. Click on "Define Brightness &…"3. For each channel, change the B&C

and press OK on the popup4. The settings appear on a Window

called "Common Tools"5. Click on "…on the current image"

to apply6. Apply it on a folder if desired

Before After

The settings can be saved to be reused at a different time:From the Common Tools bar, click on "Save Parameters"

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1. Select Montage Options– Settings:

• Scalebar At Image: on which image of the montage do you want the scalebar

• Choose As Rows or As Columns for the macro to determine the size needed for the montage

• Ignore LUTS except for Merged: All channels are shown in gray, expect on the merge

• Advanced Montage: You choose the style for each image in the montage:

» 1+2, 1+3, 1+2+3 creates a montage with the first two channels, the first and second channel and finally with all the channels

Make Montage

The settings can be saved to be reused at a different time:From the Common Tools bar, click on "Save Parameters"

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Montage Examples

• Dataset: Fluorescent Cells

Channel 1: Red

Channel 2: Green

Channel 3: Blue

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Montage Examples

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Montage Examples

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Montage Examples

Advanced Montage Reads:1+3, 2+3, 1+2, 1+2+3

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