Pseudo flat-field filter: documented but removed (?)

[Marco Bravi]

Dear ImageJ users,

I am a newbie in image analysis and I am trying to use ImageJ
side-by-side with the Tony Collins on-line manual
(http://www.uhnresearch.ca/wcif/imagej/).

Many of the images I need to analyse have a gradient in the background
which should be corrected by taking the flat-field.

Unfortunately, though, many of these images are part of a database which
was collected time ago; therefore, I was very interested by the
possibility of taking the pseudo flat-field approach described therein
(http://www.uhnresearch.ca/facilities/wcif/imagej/image_intensity_proce.htm#intensity_flat) However, the menu command “Process/Filters/Pseudo-flat field” which supposedly automates this process does not exist in my installation (nor in others I have set up), nor does it exist in the latest beta.

However, the pseudo flat-field calculation is also referenced in recent
messages in this mailing list.

Can you point me in the right direction? I know that I could blur the
image, but I was thinking to take a (maybe) smarter approach.

Thank you all in advance for any suggestion you may drop me.

                Marco Bravi

[Tony Collins-2]

The online manual describes the microscopy-related collection of plugins
that can be found by following the link on the front page of the online
manual. Please read the "About this manual" section of the manual.

Regards,

Tony


Marco Bravi wrote:

> Dear ImageJ users,
>
> I am a newbie in image analysis and I am trying to use ImageJ
> side-by-side with the Tony Collins on-line manual
> (http://www.uhnresearch.ca/wcif/imagej/).
>
> Many of the images I need to analyse have a gradient in the background
> which should be corrected by taking the flat-field.
>
> Unfortunately, though, many of these images are part of a database which
> was collected time ago; therefore, I was very interested by the
> possibility of taking the pseudo flat-field approach described therein
> (http://www.uhnresearch.ca/facilities/wcif/imagej/image_intensity_proce.htm#intensity_flat) However, the menu command “Process/Filters/Pseudo-flat field” which supposedly automates this process does not exist in my installation (nor in others I have set up), nor does it exist in the latest beta.
>
> However, the pseudo flat-field calculation is also referenced in recent
> messages in this mailing list.
>
> Can you point me in the right direction? I know that I could blur the
> image, but I was thinking to take a (maybe) smarter approach.
>
> Thank you all in advance for any suggestion you may drop me.
>
> Marco Bravi

--
Tony Collins, Ph.D.
Facility Manager
Wright Cell Imaging Facility
Toronto Western Research Institute
13-407 McLaughlin Pavilion
399 Bathurst Street
Toronto, ON. M5T 2S8
tel. [phone] fax: [phone]
http://www.uhnresearch.ca/wcif

[Alex Chekholko]

On 10/12/05, Marco Bravi <[hidden email]> wrote:
> Dear ImageJ users,
>
[snip]
>
> Can you point me in the right direction? I know that I could blur the
> image, but I was thinking to take a (maybe) smarter approach.
>

The "pseudo-flat" field correction is nothing more than subtracting
the Gaussian-blurred version of the image.  The command merely saves
you a few clicks.

Alex