Phriction Projects Wikis Bioimaging And Optics Platform Image Processing ImageJ/Fiji ijab-BIOP Channel Tools History Version 1 vs 18
Version 1 vs 18
Version 1 vs 18
Edits
Edits
- Edit by oburri, Version 18
- Mar 31 2022 16:48
- Edit by romainGuiet, Version 1
- Jan 26 2018 13:20
Edit Older Version 1... | Edit Current Version 18... |
Content Changes
Content Changes
=BIOP Channel Tools=
{F5942397, size=full, float, layout=right}
This ActionBar may be of some help to :
- set **LookUp Table** (LUT, ie false colors of the channels)
- set **Brightness & Contrast** of the current image or of a whole folder.
- create //complexe// **Montage Image** of the channels
On the current image {key Apply_to_image}
or a user defined folder {key Apply_to_Folder...}
Each modification can be applied indiviually in corresponding section:
- **LookUp Table Modification**
- **Brightness & Contrast Modification**
- **Montage Settings**
or together (if previously defined ) using the section `All at once...`
(IMPORTANT) An image should be open so the program knows how much channel you have to process.
It may be obvious BUT processed : Images should have the same number of Channel, come from the same batch (staining, acquisition... )
=Parameters =
Parameters are visible in an independant window.
They can be saved as a text file {key Save_Parameters}
or load to be reused {key Load_Parameters}
{F5942572, size=full}
=LookUp Table Modification=
{F5942669, size=full}
=Brightness & Contrast Modification=
=Montage Settings=
=BIOP Channel Tools=
WARNING: As of March 30th 2022, a breaking change in Fiji has caused previously saved parameters to be unreadable.
When you update, please note that the Parameters Window has slightly changed and **you will need to re-enter your settings once before being able to resave them in the new format**.
{F5942397, size=full, float, layout=right}
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 {nav Apply to Image}
- a defined folder {nav 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 {nav Apply to Image}
- a defined folder {nav Apply to Folder...}
(IMPORTANT) An image should be open so the program knows how many channels there are to process.
(NOTE) 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. [[ https://imagej.net/Following_an_update_site | To learn how to enable update sites, click here. ]]
You can find the tool under {nav Plugins > BIOP > Generic Tools > BIOP Channel Tools}
=1.Parameters =
Parameters are visible in an independent window.
They can be saved as a text file {nav Save Parameters}
and loaded to be reused {nav Load Parameters}
{F5942572, size=full}
=2.LookUp Table Modification=
==2.a.Channels LUT selection ==
{F5942669, size=full}
==2.b.Current Image ==
{F5942763, size=full}
==2.c.Folder ==
{F5942755, size=full}
=3.Brightness & Contrast Modification=
==3.a.B&C Selection ==
{F5942927, size=full}
==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 ==
{F5942995, size=full}
==4.b. Move scale bar ==
{F5943013, size=full}
==4.c. Montage Border - Space between images ==
{F5943029, size=full}
NOTE: to have white border make sure to set ForegroundColor to White
{F7887121, size=full}
==4.d. Make a square Montage ==
{F5943050, size=full}
==4.e. Individual Channel with Gray LUT ==
{F5943075, size=full}
==4.f. Advanced Montage ==
{F5943111, size=full}
==4.g. Add Legend ==
{F5943137, size=full}
= HELP =
For futher help please [[ https://biop.epfl.ch/INFO_Facility.html#staff | contact ]] us or open an issue on github.
| Main Developer | Romain Guiet, Oliver Burri|
| Maintainers | Romain Guiet, Oliver Burri|
= Repository =
You can find the source code in rBIOPCHTOOLS
=BIOP Channel Tools=
{F5942397, size=full, float, layout=right}
This ActionBar may be of some help to :
- set **LookUp Table** (LUT, ie false colors of the channels)
- set **Brightness & Contrast** of the current image or of a whole folder.
- create //complexe// **Montage Image** of the channels
On the current image {key Apply_to_image}
or a user defined folder {key Apply_to_Folder...}
Each modification can be applied indiviually in corresponding section:
- **LookUp Table Modification**
- **Brightness & Contrast Modification**
- **Montage Settings**
or together (if previously defined ) using the section `All at once...`
(IMPORTANT) An image should be open so the program knows how much channel you have to process.
It may be obvious BUT processed : Images should have the same number of Channel, come from the same batch (staining, acquisition... )
=Parameters =
Parameters are visible in an independant window.
They can be saved as a text file {key Save_Parameters}
or load to be reused {key Load_Parameters}
{F5942572, size=full}
=LookUp Table Modification=
{F5942669, size=full}
=Brightness & Contrast Modification=
=Montage Settings=
WARNING: As of March 30th 2022, a breaking change in Fiji has caused previously saved parameters to be unreadable.
When you update, please note that the Parameters Window has slightly changed and **you will need to re-enter your settings once before being able to resave them in the new format**.
{F5942397, size=full, float, layout=right}
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 {nav Apply to Image}
- a defined folder {nav 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 {nav Apply to Image}
- a defined folder {nav Apply to Folder...}
(IMPORTANT) An image should be open so the program knows how many channels there are to process.
(NOTE) 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. [[ https://imagej.net/Following_an_update_site | To learn how to enable update sites, click here. ]]
You can find the tool under {nav Plugins > BIOP > Generic Tools > BIOP Channel Tools}
=1.Parameters =
Parameters are visible in an independent window.
They can be saved as a text file {nav Save Parameters}
and loaded to be reused {nav Load Parameters}
{F5942572, size=full}
=2.LookUp Table Modification=
==2.a.Channels LUT selection ==
{F5942669, size=full}
==2.b.Current Image ==
{F5942763, size=full}
==2.c.Folder ==
{F5942755, size=full}
=3.Brightness & Contrast Modification=
==3.a.B&C Selection ==
{F5942927, size=full}
==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 ==
{F5942995, size=full}
==4.b. Move scale bar ==
{F5943013, size=full}
==4.c. Montage Border - Space between images ==
{F5943029, size=full}
NOTE: to have white border make sure to set ForegroundColor to White
{F7887121, size=full}
==4.d. Make a square Montage ==
{F5943050, size=full}
==4.e. Individual Channel with Gray LUT ==
{F5943075, size=full}
==4.f. Advanced Montage ==
{F5943111, size=full}
==4.g. Add Legend ==
{F5943137, size=full}
= HELP =
For futher help please [[ https://biop.epfl.ch/INFO_Facility.html#staff | contact ]] us or open an issue on github.
| Main Developer | Romain Guiet, Oliver Burri|
| Maintainers | Romain Guiet, Oliver Burri|
= Repository =
You can find the source code in rBIOPCHTOOLS
c4science · Help