Page MenuHomec4science

ijab-BIOP Channel Tools
Updated 560 Days AgoPublic

BIOP Channel Tools

This ActionBar can:

  • set LookUp Tables (LUT, ie false colors of the channels) for each channel
  • set Brightness & Contrast of the current image or of a whole folder for each channel.
  • create a complex Montage Image of the channels

Each modification can be applied indiviually on :

  • the current image Apply to Image
  • a defined folder Apply to Folder...

for each section:

  • LookUp Table Modification
  • Brightness & Contrast Modification
  • Montage Settings

Otherwise modification(s) can be applied together (if previously defined ) using the section All at once... on :

  • the current image Apply to Image
  • a defined folder Apply to Folder...
An image should be open so the program knows how many channels there are to process.
It may be obvious, BUT processed images should have the same number of channels and come from the same batch (staining, acquisition... )

0. Installation

Please make sure that the PTBIOP Updade Site as well as the IBMP-CNRS Update Site are enabled in FIJI. To learn how to enable update sites, click here.

You can find the tool under PluginsBIOPGeneric ToolsBIOP Channel Tools

1.Parameters

Parameters are visible in an independent window.
They can be saved as a text file Save Parameters
and loaded to be reused Load Parameters

2.LookUp Table Modification

2.a.Channels LUT selection

2.b.Current Image

2.c.Folder

3.Brightness & Contrast Modification

3.a.B&C Selection

3.b.Current Image

Please c.f. 2.b

3.c.Folder

Please c.f. 3.b

4.Montage Settings

Many options are available, please find here (just) some examples.

4.a.Default

4.b. Move scale bar

4.c. Montage Border - Space between images

NOTE: to have white border make sure to set ForegroundColor to White

4.d. Make a square Montage

4.e. Individual Channel with Gray LUT

4.f. Advanced Montage

4.g. Add Legend

HELP

For futher help please contact us or open an issue on github.

Main DeveloperRomain Guiet, Oliver Burri
MaintainersRomain Guiet, Oliver Burri

Repository

You can find the source code in rBIOPCHTOOLS

Last Author
chiarutt
Last Edited
May 15 2019, 14:38

Event Timeline

romainGuiet created this document.Jan 26 2018, 13:20
romainGuiet edited the content of this document. (Show Details)
romainGuiet edited the content of this document. (Show Details)Jan 26 2018, 13:31
romainGuiet edited the content of this document. (Show Details)Jan 26 2018, 14:15
romainGuiet edited the content of this document. (Show Details)Jan 26 2018, 14:19
romainGuiet edited the content of this document. (Show Details)Jan 26 2018, 14:23
oburri edited the content of this document. (Show Details)Jan 26 2018, 14:32
romainGuiet edited the content of this document. (Show Details)Jan 26 2018, 14:39
romainGuiet edited the content of this document. (Show Details)
oburri edited the content of this document. (Show Details)Jan 26 2018, 15:00
oburri added a project: Restricted Project.
oburri edited the content of this document. (Show Details)Jan 26 2018, 16:16
oburri edited the content of this document. (Show Details)May 7 2018, 09:26
oburri edited the content of this document. (Show Details)May 7 2018, 09:30
romainGuiet edited the content of this document. (Show Details)Jun 1 2018, 09:13
romainGuiet edited the content of this document. (Show Details)Jun 1 2018, 09:17
romainGuiet edited the content of this document. (Show Details)
chiarutt edited the content of this document. (Show Details)May 15 2019, 14:38