Re: ImageJ projection of 4D stack

[Aryeh Weiss]

I have a question about Image5D similar to the question below. I want to
take an XYZT series, and reduce it to XYT by running the extended depth
of field plugin on the z-stacks. Can this be done in Image5D, of has
someone done something similar?

--aryeh

On Sat, 9 Dec 2006 18:15:53 +0100, Joachim Walter <[hidden email]-
MUENCHEN.DE> wrote:

>You can use the Image5D plugin.
>- If you have your data as separate 2D TIFF images all in one directory,
>you open them with the Virtual Image5D opener.
>- Click on the "Color" button and assign a color to each channel (not
>limited to RGB)
>- Use "Z Project" of the Image5D plugins. In the window that pops up you
>have to select "All Time Frames".
>The resulting series of projections has to fit in memory, though.
>
>
>Rainer Kohler schrieb:
>> Hi,
>>
>> I have a time series of image stacks with three channels from
>> FluoView. Size 1 GB.
>> How can I project the z-stacks to create a time series of the
>> projections of merged images as well as of the separate channels.
>> Because of memory restrictions it seems not to work in FluoView.
>> Could I do it in ImageJ?

[Joachim Walter]

Aryeh,

here is a short macro to do this with the "Stack Focuser", which also
does Extended Depht of Field. The EPFL Extended Depht of Field Plugin is
not macro scriptable.

Wayne, there is currently no way to retrieve the number of channels or
frames of an Image in a macro. Could you add "nChannels" and "nFrames"
commands similar to the "nSlices" command?

Best wishes,
Joachim



// Macro start
idOrig = getImageID();
name = getTitle();
nFrames = 7;

run("New Image5D", "name="+name+"-ExtDepth type=8-bit fill=Black
width=256 height=256 channels=1 slices=1 frames="+nFrames);
idExtDepth = getImageID();

for (i=1; i<=nFrames; i++) {
  selectImage(idOrig);
  run("Set Position", "frame="+i);
  run("Stack Focuser ", "enter=11");
  run("Select All");
  run("Copy");
  run("Close");
  selectImage(idExtDepth);
  run("Set Position", "frame="+i);
  run("Paste");
}

Aryeh Weiss schrieb:

> I have a question about Image5D similar to the question below. I want to
> take an XYZT series, and reduce it to XYT by running the extended depth
> of field plugin on the z-stacks. Can this be done in Image5D, of has
> someone done something similar?
>
> --aryeh
>
> On Sat, 9 Dec 2006 18:15:53 +0100, Joachim Walter <[hidden email]-
> MUENCHEN.DE> wrote:
>
>  
>> You can use the Image5D plugin.
>> - If you have your data as separate 2D TIFF images all in one directory,
>> you open them with the Virtual Image5D opener.
>> - Click on the "Color" button and assign a color to each channel (not
>> limited to RGB)
>> - Use "Z Project" of the Image5D plugins. In the window that pops up you
>> have to select "All Time Frames".
>> The resulting series of projections has to fit in memory, though.
>>
>>
>> Rainer Kohler schrieb:
>>    
>>> Hi,
>>>
>>> I have a time series of image stacks with three channels from
>>> FluoView. Size 1 GB.
>>> How can I project the z-stacks to create a time series of the
>>> projections of merged images as well as of the separate channels.
>>> Because of memory restrictions it seems not to work in FluoView.
>>> Could I do it in ImageJ?
>>>      

--
-----------------------------------------------
Dr. Joachim Walter

TILL I.D. GmbH
c\o BioImaging Zentrum
Großhaderner Str. 2
D-82152 Martinsried

Tel.: [phone]
Fax:  [phone]
 
Geschäftsführer: Dr. Rainer Uhl
HRB 129399 Amtsgericht München
USt.-IdNr. DE 205045721

[Aryeh Weiss]

Quoting Joachim Walter <[hidden email]>:

> Aryeh,
>
> here is a short macro to do this with the "Stack Focuser", which also
> does Extended Depht of Field. The EPFL Extended Depht of Field Plugin
> is not macro scriptable.
>
> Wayne, there is currently no way to retrieve the number of channels or
> frames of an Image in a macro. Could you add "nChannels" and "nFrames"
> commands similar to the "nSlices" command?
>

Thank you Joachim. This is exactly what I needed to get me started.
Could the stack focuser be grafted into the z-project plugin of the  
Image5D package? In that case it would have all of the slice and frame  
info that it needs.

--aryeh
--
Aryeh Weiss
School of Engineering
Bar Ilan University


----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.

[Wayne Rasband]

ImageJ 1.38s, due next week, adds a getDimensions(width, hight,
channels, slices, frames) macro function. Here is an updated version of
Joachim's macro that uses the "Stack Focuser" plugin to reduce an XYCZT
stack to XYCT.

   requires("1.38s");
   id = getImageID();
   getDimensions(width, hight, channels, slices, frames);
   run("New Image5D", "name="+getTitle+"-ExtDepth type="
     +bitDepth+"-bit fill=Black width=256 height=256 channels="
     +channels+" slices=1 frames="+frames);
   id2 = getImageID();
   setBatchMode(true);
   for (i=1; i<=frames; i++) {
      for (ch=1; ch<=channels; ch++) {
         selectImage(id);
         run("Set Position", "channel="+ch+" frame="+i);
         run("Stack Focuser ", "enter=11");
         run("Copy");
         close;
         selectImage(id2);
         run("Set Position", "channel="+ch+" frame="+i);
         run("Paste");
      }
   }
   resetMinAndMax;

-wayne

On May 14, 2007, at 5:38 AM, Joachim Walter wrote:

> Aryeh,
>
> here is a short macro to do this with the "Stack Focuser", which also
> does Extended Depht of Field. The EPFL Extended Depht of Field Plugin
> is not macro scriptable.
>
> Wayne, there is currently no way to retrieve the number of channels or
> frames of an Image in a macro. Could you add "nChannels" and "nFrames"
> commands similar to the "nSlices" command?
>
> Best wishes,
> Joachim
>
>
>
> // Macro start
> idOrig = getImageID();
> name = getTitle();
> nFrames = 7;
>
> run("New Image5D", "name="+name+"-ExtDepth type=8-bit fill=Black
> width=256 height=256 channels=1 slices=1 frames="+nFrames);
> idExtDepth = getImageID();
>
> for (i=1; i<=nFrames; i++) {
>  selectImage(idOrig);
>  run("Set Position", "frame="+i);
>  run("Stack Focuser ", "enter=11");
>  run("Select All");
>  run("Copy");
>  run("Close");
>  selectImage(idExtDepth);
>  run("Set Position", "frame="+i);
>  run("Paste");
> }
>
> Aryeh Weiss schrieb:
>> I have a question about Image5D similar to the question below. I want
>> to take an XYZT series, and reduce it to XYT by running the extended
>> depth of field plugin on the z-stacks. Can this be done in Image5D,
>> of has someone done something similar?
>> --aryeh
>>
>> On Sat, 9 Dec 2006 18:15:53 +0100, Joachim Walter <[hidden email]-
>> MUENCHEN.DE> wrote:
>>
>>
>>> You can use the Image5D plugin.
>>> - If you have your data as separate 2D TIFF images all in one
>>> directory,
>>> you open them with the Virtual Image5D opener.
>>> - Click on the "Color" button and assign a color to each channel (not
>>> limited to RGB)
>>> - Use "Z Project" of the Image5D plugins. In the window that pops up
>>> you
>>> have to select "All Time Frames".
>>> The resulting series of projections has to fit in memory, though.
>>>
>>>
>>> Rainer Kohler schrieb:
>>>
>>>> Hi,
>>>>
>>>> I have a time series of image stacks with three channels from
>>>> FluoView. Size 1 GB.
>>>> How can I project the z-stacks to create a time series of the
>>>> projections of merged images as well as of the separate channels.
>>>> Because of memory restrictions it seems not to work in FluoView.
>>>> Could I do it in ImageJ?
>>>>
>
>
> --
> -----------------------------------------------
> Dr. Joachim Walter
>
> TILL I.D. GmbH
> c\o BioImaging Zentrum
> Großhaderner Str. 2
> D-82152 Martinsried
>
> Tel.: [phone]
> Fax:  [phone]
> Geschäftsführer: Dr. Rainer Uhl
> HRB 129399 Amtsgericht München
> USt.-IdNr. DE 205045721
>

[Aryeh Weiss]

Wayne Rasband wrote:
> ImageJ 1.38s, due next week, adds a getDimensions(width, hight,
> channels, slices, frames) macro function. Here is an updated version of
> Joachim's macro that uses the "Stack Focuser" plugin to reduce an XYCZT
> stack to XYCT.
>

Thank you Wayne. I was floored when I had a reply from Joachim that enabled me
to solve my problem that day, even if I needed to prompt the user for nFrames.
With this function I wont even have to do that. The quick responses from you and
other members of this list never cease to amaze me.

--aryeh
--
Aryeh Weiss
School of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

[Knecht, David]

I am trying to do an extended depth of focus on a stack.  I found this  
macro from Joachim to do the job, but it is set for 256x256 and 7  
frames.  Is there a way to make this general or another way to do EDF  
on a stack?  Thanks- Dave

Begin forwarded message:

> From: Joachim Walter <[hidden email]>
> Date: May 14, 2007 5:38:09 AM EDT
> To: [hidden email]
> Subject: Re: ImageJ projection of 4D stack
> Reply-To: ImageJ Interest Group <[hidden email]>
>
> Aryeh,
>
> here is a short macro to do this with the "Stack Focuser", which  
> also does Extended Depht of Field. The EPFL Extended Depht of Field  
> Plugin is not macro scriptable.
>
> Wayne, there is currently no way to retrieve the number of channels  
> or frames of an Image in a macro. Could you add "nChannels" and  
> "nFrames" commands similar to the "nSlices" command?
>
> Best wishes,
> Joachim
>
>
>
> // Macro start
> idOrig = getImageID();
> name = getTitle();
> nFrames = 7;
>
> run("New Image5D", "name="+name+"-ExtDepth type=8-bit fill=Black  
> width=256 height=256 channels=1 slices=1 frames="+nFrames);
> idExtDepth = getImageID();
>
> for (i=1; i<=nFrames; i++) {
> selectImage(idOrig);
> run("Set Position", "frame="+i);
> run("Stack Focuser ", "enter=11");
> run("Select All");
> run("Copy");
> run("Close");
> selectImage(idExtDepth);
> run("Set Position", "frame="+i);
> run("Paste");
> }
>
> Aryeh Weiss schrieb:
>> I have a question about Image5D similar to the question below. I  
>> want to take an XYZT series, and reduce it to XYT by running the  
>> extended depth of field plugin on the z-stacks. Can this be done in  
>> Image5D, of has someone done something similar?
>> --aryeh
>>
>> On Sat, 9 Dec 2006 18:15:53 +0100, Joachim Walter <[hidden email]-
>> MUENCHEN.DE> wrote:
>>
>>
>>> You can use the Image5D plugin.
>>> - If you have your data as separate 2D TIFF images all in one  
>>> directory,
>>> you open them with the Virtual Image5D opener.
>>> - Click on the "Color" button and assign a color to each channel  
>>> (not
>>> limited to RGB)
>>> - Use "Z Project" of the Image5D plugins. In the window that pops  
>>> up you
>>> have to select "All Time Frames".
>>> The resulting series of projections has to fit in memory, though.
>>>
>>>
>>> Rainer Kohler schrieb:
>>>
>>>> Hi,
>>>>
>>>> I have a time series of image stacks with three channels from
>>>> FluoView. Size 1 GB.
>>>> How can I project the z-stacks to create a time series of the
>>>> projections of merged images as well as of the separate channels.
>>>> Because of memory restrictions it seems not to work in FluoView.
>>>> Could I do it in ImageJ?
>>>>
>
>
> --
> -----------------------------------------------
> Dr. Joachim Walter
>
> TILL I.D. GmbH
> c\o BioImaging Zentrum
> Großhaderner Str. 2
> D-82152 Martinsried
>
> Tel.: [phone]
> Fax:  [phone]
> Geschäftsführer: Dr. Rainer Uhl
> HRB 129399 Amtsgericht München
> USt.-IdNr. DE 205045721

Dr. David Knecht
Department of Molecular and Cell Biology
Co-head Flow Cytometry and Confocal Microscopy Facility
U-3125
91 N. Eagleville Rd.
University of Connecticut
Storrs, CT 06269
860-486-2200
860-486-4331 (fax)

[Aryeh Weiss]

Wayne (almost immediately) added the required functionality to allow teh
macro to get all of the information that it needs. I attached a version
that will determine the number of slices and other relevant dimensions.
I have not used it for a while, so I am not sure that it still works
without modification, but it shoudl show you what you need to do.

--aryeh

David Knecht wrote:

> I am trying to do an extended depth of focus on a stack.  I found this
> macro from Joachim to do the job, but it is set for 256x256 and 7
> frames.  Is there a way to make this general or another way to do EDF on
> a stack?  Thanks- Dave
>
> Begin forwarded message:
>
>> From: Joachim Walter <[hidden email]>
>> Date: May 14, 2007 5:38:09 AM EDT
>> To: [hidden email]
>> Subject: Re: ImageJ projection of 4D stack
>> Reply-To: ImageJ Interest Group <[hidden email]>
>>
>> Aryeh,
>>
>> here is a short macro to do this with the "Stack Focuser", which also
>> does Extended Depht of Field. The EPFL Extended Depht of Field Plugin
>> is not macro scriptable.
>>
>> Wayne, there is currently no way to retrieve the number of channels or
>> frames of an Image in a macro. Could you add "nChannels" and "nFrames"
>> commands similar to the "nSlices" command?
>>
>> Best wishes,
>> Joachim
>>
>>
>>
>> // Macro start
>> idOrig = getImageID();
>> name = getTitle();
>> nFrames = 7;
>>
>> run("New Image5D", "name="+name+"-ExtDepth type=8-bit fill=Black
>> width=256 height=256 channels=1 slices=1 frames="+nFrames);
>> idExtDepth = getImageID();
>>
>> for (i=1; i<=nFrames; i++) {
>> selectImage(idOrig);
>> run("Set Position", "frame="+i);
>> run("Stack Focuser ", "enter=11");
>> run("Select All");
>> run("Copy");
>> run("Close");
>> selectImage(idExtDepth);
>> run("Set Position", "frame="+i);
>> run("Paste");
>> }
>>
>> Aryeh Weiss schrieb:
>>> I have a question about Image5D similar to the question below. I want
>>> to take an XYZT series, and reduce it to XYT by running the extended
>>> depth of field plugin on the z-stacks. Can this be done in Image5D,
>>> of has someone done something similar?
>>> --aryeh
>>>
>>> On Sat, 9 Dec 2006 18:15:53 +0100, Joachim Walter <[hidden email]-
>>> MUENCHEN.DE> wrote:
>>>
>>>
>>>> You can use the Image5D plugin.
>>>> - If you have your data as separate 2D TIFF images all in one
>>>> directory,
>>>> you open them with the Virtual Image5D opener.
>>>> - Click on the "Color" button and assign a color to each channel (not
>>>> limited to RGB)
>>>> - Use "Z Project" of the Image5D plugins. In the window that pops up
>>>> you
>>>> have to select "All Time Frames".
>>>> The resulting series of projections has to fit in memory, though.
>>>>
>>>>
>>>> Rainer Kohler schrieb:
>>>>
>>>>> Hi,
>>>>>
>>>>> I have a time series of image stacks with three channels from
>>>>> FluoView. Size 1 GB.
>>>>> How can I project the z-stacks to create a time series of the
>>>>> projections of merged images as well as of the separate channels.
>>>>> Because of memory restrictions it seems not to work in FluoView.
>>>>> Could I do it in ImageJ?
>>>>>
>>
>>
>> --
>> -----------------------------------------------
>> Dr. Joachim Walter
>>
>> TILL I.D. GmbH
>> c\o BioImaging Zentrum
>> Großhaderner Str. 2
>> D-82152 Martinsried
>>
>> Tel.: [phone]
>> Fax:  [phone]
>> Geschäftsführer: Dr. Rainer Uhl
>> HRB 129399 Amtsgericht München
>> USt.-IdNr. DE 205045721
>
> Dr. David Knecht
> Department of Molecular and Cell Biology
> Co-head Flow Cytometry and Confocal Microscopy Facility
> U-3125
> 91 N. Eagleville Rd.
> University of Connecticut
> Storrs, CT 06269
> 860-486-2200
> 860-486-4331 (fax)
>

--
Aryeh Weiss
School of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]


  requires("1.38s");
  id = getImageID();
  getDimensions(width, height, channels, slices, frames);
  run("New Image5D", "name="+getTitle+"-ExtDepth type="
    +bitDepth+"-bit fill=Black width="+width+" height="+height+" channels="
    +channels+" slices=1 frames="+frames);
  id2 = getImageID();
  setBatchMode(true);
 
  for (i=1; i<=frames; i++) {
     for (ch=1; ch<=channels; ch++) {
        selectImage(id);
        run("Set Position", "channel="+ch+" frame="+i);
        run("Median...", "radius=1 stack");
        run("Stack Focuser ", "enter=5");
        run("Copy");
        close;
        selectImage(id2);
        run("Set Position", "channel="+ch+" frame="+i);
        run("Paste");
          resetMinAndMax;
        run("Grays");
     }
 
 // resetMinAndMax;
// run("Grays");
}