batch adjusting lookup tables, b/c & making montagesbiop.epfl.ch/pdf/common...
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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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