Existing efficient macro/plugin for transposing stack/hyperstack

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

Existing efficient macro/plugin for transposing stack/hyperstack

Jeff Hardin
Dear Imagers,
I’m looking for existing code that will take an AxB stack/hyperstack and transpose its entries to a BxA hyperstack. This is useful if a large 4d dataset is already in an A time points of a single focal plane x B focal planes format, but should be in a B focal planes x A time points per focal format.
If the code works on a large stack that can be read in as a Virtual Stack, that would be awesome (my example is a QuickTime movie that has 8100 frames).
Cheers,
Jeff
__________________________
Jeff Hardin
Raymond E. Keller Professor and Chair
Department of Integrative Biology
University of Wisconsin
1117 W. Johnson St.
Madison, WI 53706
voice: (608) 262-9634
fax: (608) 262-7319
email: [hidden email]<mailto:[hidden email]>
web page: http://worms.zoology.wisc.edu

On Sep 19, 2017, at 4:13 PM, IMAGEJ automatic digest system <[hidden email]<mailto:[hidden email]>> wrote:

There are 14 messages totaling 10379 lines in this issue.

Topics in this special issue:

 1. Starting with Fiji
 2. question about plot API
 3. move displayed area to find a marker
 4. Announcement: Digital Image Analysis with ImageJ Workshop Nov 7/8/9
 5. ImageJ Compile&Run compiles java program in editor but runs from cache.
    How to fix? (7)
 6. Segmentation Editor: Save/Load/Import?
 7. Any suggestions for the estimate of domain size? (2)

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

----------------------------------------------------------------------

Date:    Tue, 19 Sep 2017 04:54:59 +0000
From:    T Purushotham <[hidden email]<mailto:[hidden email]>>
Subject: Starting with Fiji

Respected to all,
Greetings of the day. I have lot of case images of fetal echo with different types like four chamber view, LVOT, RVOT, Three vessel view and Three vessel arch view.Now, I want to develop a macro or algorithm in such a way that, whenever I upload the image  it can automatically identifies the image whether it belongs to which type in above mentioned five cases.
                Can  anyone help me to move forward in this. Also, how far this ImageJ/Fijji useful for me to overcome my problem. Mention any new Machine Learning strategies to solve this.

Thanks and Regards,
T Purushotham,
IIT- Madras.


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

Date:    Mon, 18 Sep 2017 15:53:17 +0200
From:    Michael Schmid <[hidden email]<mailto:[hidden email]>>
Subject: Re: question about plot API

Hi Aryeh,

currently, the ImageJ Plot class only has CONNECTED_CIRCLES, no
CONNECTED_TRIANGLES, CONNECTED_CROSSES or so.
I don't think that connected dots would make much sense (the line would
hide the dots).  One could think of connected boxes or diamonds [oops, I
just see that we even don't have plain diamonds yet!]
Beyond ImageJ, I have seen much more plots with connected circles
compared to other connected symbols, so I consider this not too bad a
choice.
Also, the CONNECTED_CIRCLES are still not as nice as those of some other
plotting programs; I think it would be nicer to have the lines end just
outside the circles, not go all the way to the centers (if I have much
time, maybe I'll change this).  But what we have is better than nothing.


If you want, e.g., connected squares, you could plot the same data set
twice, once as squares (BOX), then as a line.

In any case, ImageJ is not a full-fledged plotting program; if you need
advanced plots you will still need Gnuplot, Grace, Veusz, etc, or the
expensive solution named Origin.


Michael
________________________________________________________________
On 18/09/2017 14:14, Aryeh Weiss wrote:
I have not been able to figure out how to plot connected markers,
other than circles. For example:

plt.addPoints(range(1,14), dsum, None, Plot.CONNECTED_CIRCLES, "Total
Area")

adds a trace to plt. However, in another line, I have

plt.addPoints(range(1,14),[x/tmp[0] for x in tmp], None,  i%8 ,
"Track "+ str(i))

where I use i%8 to cycle through the various markers (CROSS, DOT,
TRIANGLE, etc).
and I would like to plot these connected, just like the connected
circles, but I cannot find the option to do that.

A second question is how to use the labels that are in the last
argument of the addPoints command. I would like to put them in the
legend, but I do not see how to recover them in order to add them to the
addLegend command.

Thanks in advance for any help on these issues.

--aryeh


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

Date:    Mon, 18 Sep 2017 09:50:20 +0200
From:    Michael Schmid <[hidden email]<mailto:[hidden email]>>
Subject: Re: move displayed area to find a marker

Hi Csaba,

here is a simple macro that takes a point selection with several points
and zooms on each of them, one after the other, each time you press the
F8 key.
(you have to install the macro or include it in your StatupMacros)

//global variables, these are remembered
var xpoints = newArray(0);  //empty array
var ypoints;
var pointIndex;
var zoom = 18; //actual zoom level will be slightly less, 16x

macro "zoomOnPoints [F8]" {
  if (pointIndex >= xpoints.length) {
    if (selectionType() != 10)
      exit("Multipoint selection needed to start");
    getSelectionCoordinates(xpoints, ypoints);
    pointIndex = 0;
  }
  getLocationAndSize(x, y, width, height); //window size
  x = xpoints[pointIndex];
  y = ypoints[pointIndex];
  w = width/zoom;
  h = height/zoom;
  makeRectangle(x-w/2, y-w/2, w, h);
  run("To Selection");  //zoom to selection
  run("Restore Selection");
  pointIndex++;
}


Michael
________________________________________________________________

On 14/09/2017 09:25, Csaba DÁVID wrote:
Hi,i would like write a macro to find markers (point selection ROIs)
that were set earlier on an image. I would like to see them on the
zoomed image. Unfortunately, when i click on a ROI in the ROI manager,
it can set the layer, but it cannot set the location. The same if I do
it with a macro. Is there any command, which moves the displayed are to
specified coordinates? It would be extremely useful if i could jump from
one ROI location to the next one without zooming out and zooming in
again.Csaba

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

Date:    Tue, 19 Sep 2017 10:49:42 -0400
From:    Lai Ding <[hidden email]<mailto:[hidden email]>>
Subject: Announcement: Digital Image Analysis with ImageJ Workshop Nov 7/8/9

Dear Everyone,

The NeuroTechnology Studio at BWH will host a 3-day ImageJ workshop in November 2017. Detailed information is below.

Digital Image Analysis with ImageJ
November 7th – 9th   2017

This intensive 3-day workshop taught by Dr. Lai Ding, Senior Imaging Scientist of the NeuroTechnology Studio(formerly manager of the Harvard NeuroDiscovery Center Enhanced Neuroimaging Core), introduces ImageJ, its basic functions, and its macro programming capabilities. Using real imaging projects, Dr. Ding will demonstrate common image analysis tasks such as basic image processing, stack alignment, cell counting and measurement. Macro writing will be covered to demonstrate how to automate a series of ImageJ commands, to process massive datasets automatically and to store results as desired.

The workshop is broken down into three sessions. Interested participants can sign up for one or more sessions depending on their interest and experience. See tentative schedule below.
If you are interested in this workshop but unable to join this time, please also let us know (email [hidden email]<mailto:[hidden email]>) if you may be able to join the same workshop in the coming months. We MAY host another identical workshop in near future based on the interests shown.
----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- -----
Program Schedule:
Session I (November 7th ) ImageJ for beginners: basic ImageJ functions, measurement, filtering, background subtraction, cell counting, particle analysis, and ethics on image processing.

Session II (November 8th ) Advanced ImageJ: morphology filter, thresholding methods, using ImageJ on FRAP, colocalization analysis and wound assay, working with plugins, designing image analysis protocols.

Session III (November 9th ) ImageJ Macro Programming: introduce ImageJ macro programming language, record image process protocols as macro, batch process multiple images, user interactive features in macro, case study with sample codes. This session is aimed towards the non-programmer, however we do expect the participant to have a basic idea of programming flow control syntax ("for" loop, "if-else" control). The participants are strongly encouraged to go through a brief tutorial on the ImageJ official website before the workshop. http://rsb.info.nih.gov/ij/developer/macro/macros.html

Workshop Location:
L2-025
Countway Library Computer Classroom
Harvard Medical School
10 Shattuck St.
Boston, MA 02115


To register, please complete the online registration form by clicking
https://docs.google.com/forms/d/1n3n5tzSR_MM45NqkF1gW4JTa2SfhnaKNEkrry0H5X7o/

For further information please contact: Lai Ding at [hidden email]


Best Regards
Lai Ding

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

Date:    Mon, 18 Sep 2017 23:04:26 -0400
From:    Fred <[hidden email]>
Subject: ImageJ Compile&Run compiles java program in editor but runs from cache. How to fix?

I have been successfully Compile&Run(ing) a Java plugin from the ImageJ editor. At one point the plugin seemed to be in an infinite loop (using massive CPU and not responding to gui interactions). I killed the ImageJ process, and then restarted ImageJ.  Now imagej only runs the version of the program, i.e., class files, that existed when I start imagej.

I can make changes and 'Compile and Run...' .  The java program(s) will compile. Although the program, i.e., class files, that is run is the one that existed when imagej started   I suspect that imagej is caching the class files for some reason, but the cache is prevented from being updated.  Where is this cache or how to get imagej to compile and RUN the program from the editor?

Thanks in advance,

Fred

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

Date:    Tue, 19 Sep 2017 16:33:03 +0100
From:    Gabriel Landini <[hidden email]>
Subject: Re: ImageJ Compile&Run compiles java program in editor but runs from cache. How to fix?

You need to restart ImageJ or run Refresh Menus, (although I seem to remember
somebody commenting that restarting is better).
Cheers

Gabriel


On Tuesday, 19 September 2017 04:04:26 BST you wrote:
I have been successfully Compile&Run(ing) a Java plugin from the ImageJ
editor. At one point the plugin seemed to be in an infinite loop (using
massive CPU and not responding to gui interactions). I killed the ImageJ
process, and then restarted ImageJ.  Now imagej only runs the version of
the program, i.e., class files, that existed when I start imagej.

I can make changes and 'Compile and Run...' .  The java program(s) will
compile. Although the program, i.e., class files, that is run is the one
that existed when imagej started   I suspect that imagej is caching the
class files for some reason, but the cache is prevented from being updated.
Where is this cache or how to get imagej to compile and RUN the program
from the editor?

Thanks in advance,

Fred

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

Date:    Tue, 19 Sep 2017 08:27:23 -0700
From:    kscaplen16 <[hidden email]>
Subject: Re: Segmentation Editor: Save/Load/Import?

Hi Daniel and Bene,

I realize this is an old post, but I was wondering if either of you ever got
Amira to work with segmentation editor. I am interested in doing exactly
what Daniel has proposed: to save and load a current segmentation or even
save a finalized segmentation so that I can analyze or reanalyze it at a
later time (in 3D ROI manager). Thus far, I am able to save the labels (as a
tiff file), which is basically the black screen with my labeled segments,
but I am not able to merge it with the actual file that was segmented (the
file that has my brain image).

I have downloaded the Amira reader and writer plugins to save my
segmentation progress, but Segmentation Editor doesn't seem to recognize the
loaded file. Do either of you have any idea as to what I am doing wrong.

Thanks so much in advance for your insight!
Kristin



--
Sent from: http://imagej.1557.x6.nabble.com/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

Date:    Tue, 19 Sep 2017 10:56:01 -0500
From:    Fred Damen <[hidden email]>
Subject: Re: ImageJ Compile&Run compiles java program in editor but runs from cache. How to fix?

The whole point is that I should not have to restart imagej every time I need
to recompile a Java plugin.  And up to the point that I needed to kill imagej
I did not need to restart.  Help->Refresh Menus does not cause the newer
version of the plugin to be used.

Thanks,

Fred

On Tue, September 19, 2017 10:33 am, Gabriel Landini wrote:
You need to restart ImageJ or run Refresh Menus, (although I seem to remember
somebody commenting that restarting is better).
Cheers

Gabriel


On Tuesday, 19 September 2017 04:04:26 BST you wrote:
I have been successfully Compile&Run(ing) a Java plugin from the ImageJ
editor. At one point the plugin seemed to be in an infinite loop (using
massive CPU and not responding to gui interactions). I killed the ImageJ
process, and then restarted ImageJ.  Now imagej only runs the version of
the program, i.e., class files, that existed when I start imagej.

I can make changes and 'Compile and Run...' .  The java program(s) will
compile. Although the program, i.e., class files, that is run is the one
that existed when imagej started   I suspect that imagej is caching the
class files for some reason, but the cache is prevented from being updated.
Where is this cache or how to get imagej to compile and RUN the program
from the editor?

Thanks in advance,

Fred

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

Date:    Tue, 19 Sep 2017 17:42:08 +0100
From:    Gabriel Landini <[hidden email]>
Subject: Re: ImageJ Compile&Run compiles java program in editor but runs from cache. How to fix?

On Tuesday, 19 September 2017 16:56:01 BST [hidden email] wrote:
The whole point is that I should not have to restart imagej every time I
need to recompile a Java plugin.  And up to the point that I needed to kill
imagej I did not need to restart.  Help->Refresh Menus does not cause the
newer version of the plugin to be used.

So you mean that the program was modified AND compiled, but the code that runs
is the old one?
I would check the date of the class file. Maybe the last time it did no
compile? Or maybe there is more than one installation of IJ (I have seen that
several times, people copying plugins in the plugin folder but which never
appear in the menu... and then realise that there were 2 copies of IJ!

Cheers

Gabriel

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

Date:    Tue, 19 Sep 2017 18:21:40 +0200
From:    Michael Schmid <[hidden email]>
Subject: Re: ImageJ Compile&Run compiles java program in editor but runs from cache. How to fix?

Hi Fred,

in my experience, 'Compile&Run' recompiles source files that are newer
than the corresponding .class files. This is true for all classes that
are called from the main class (the one you select with 'Compile&Run'),
not recursively for others.

So if you have
 My_Plugin, calling
   SubClass1, calling
     SubClass2
and My_Plugin has no reference to SubClass2,
then ImageJ won't compile SubClass2, even if SubClass2.java is newer
than SubClass2.class.

To make sure, just delete all .class files, then ImageJ will recompile all.


Michael
________________________________________________________________
On 19/09/2017 05:04, Fred wrote:
I have been successfully Compile&Run(ing) a Java plugin from the ImageJ editor. At one point the plugin seemed to be in an infinite loop (using massive CPU and not responding to gui interactions). I killed the ImageJ process, and then restarted ImageJ.  Now imagej only runs the version of the program, i.e., class files, that existed when I start imagej.

I can make changes and 'Compile and Run...' .  The java program(s) will compile. Although the program, i.e., class files, that is run is the one that existed when imagej started   I suspect that imagej is caching the class files for some reason, but the cache is prevented from being updated.  Where is this cache or how to get imagej to compile and RUN the program from the editor?

Thanks in advance,

Fred

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

Date:    Tue, 19 Sep 2017 12:33:07 -0500
From:    Fred Damen <[hidden email]>
Subject: Re: ImageJ Compile&Run compiles java program in editor but runs from cache. How to fix?

Greetings Gabriel,

There is only one copy of ImageJ.  The problem did not exist before I killed
imagej while it was stuck. The problem existed after and no other changes have
been made, except to the source code of the plugin in question.

The plugin recompiles, timestamps of the class files and java files are when I
hit Ctrl-R.  As tests, I inserted a syntax error into the source, hit Ctrl-R,
and the error window pops up correctly identifying the syntax error; I erased
the .class files while imagej is running and ran the plugin from the Plugins
menu and the version that existed when imagej started was run; *without the
.class files in the plugins directory*.  This leads me to believe that there
is a cache somewhere; which I can not find.

When I start imagej with the .class files in the plugins directory the .class
files seem to get placed in some cache somewhere, once they are there they do
not get updated.  Running the Help->Refresh Menus with the .class files cached
the version that runs is not updated.  As a new test I tried, exiting imagej,
erase .class files, start imagej; the plugin does not show up in the Plugins
menu; then I update the plugin, i.e., change a string in a IJ.log, Ctrl-R,
Help->Refresh Menus; the plugin now shows up in the Plugins menu and it runs
the current version.  Make another update, Ctrl-R, and it runs the previous
version.

Fred


On Tue, September 19, 2017 11:42 am, Gabriel Landini wrote:
On Tuesday, 19 September 2017 16:56:01 BST [hidden email] wrote:
The whole point is that I should not have to restart imagej every time I
need to recompile a Java plugin.  And up to the point that I needed to kill
imagej I did not need to restart.  Help->Refresh Menus does not cause the
newer version of the plugin to be used.

So you mean that the program was modified AND compiled, but the code that runs
is the old one?
I would check the date of the class file. Maybe the last time it did no
compile? Or maybe there is more than one installation of IJ (I have seen that
several times, people copying plugins in the plugin folder but which never
appear in the menu... and then realise that there were 2 copies of IJ!

Cheers

Gabriel

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

Date:    Tue, 19 Sep 2017 15:20:54 -0500
From:    Fred Damen <[hidden email]>
Subject: Re: ImageJ Compile&Run compiles java program in editor but runs from cache. How to fix?

I read a little imagej code and came upon:
/** This version of the constructor is used when ImageJ is launched using Java
WebStart. */
public PluginClassLoader(String path, boolean callSuper) {
super(new URL[0], Thread.currentThread().getContextClassLoader());
init(path);
}

Which seems like it might be using a cache class loader if 'Java WebStart' is
turned on.  How do I tell if it is on and how can it be turned off?

Thanks,

Fred

On Tue, September 19, 2017 12:33 pm, Fred Damen wrote:
Greetings Gabriel,

There is only one copy of ImageJ.  The problem did not exist before I killed
imagej while it was stuck. The problem existed after and no other changes have
been made, except to the source code of the plugin in question.

The plugin recompiles, timestamps of the class files and java files are when I
hit Ctrl-R.  As tests, I inserted a syntax error into the source, hit Ctrl-R,
and the error window pops up correctly identifying the syntax error; I erased
the .class files while imagej is running and ran the plugin from the Plugins
menu and the version that existed when imagej started was run; *without the
.class files in the plugins directory*.  This leads me to believe that there
is a cache somewhere; which I can not find.

When I start imagej with the .class files in the plugins directory the .class
files seem to get placed in some cache somewhere, once they are there they do
not get updated.  Running the Help->Refresh Menus with the .class files cached
the version that runs is not updated.  As a new test I tried, exiting imagej,
erase .class files, start imagej; the plugin does not show up in the Plugins
menu; then I update the plugin, i.e., change a string in a IJ.log, Ctrl-R,
Help->Refresh Menus; the plugin now shows up in the Plugins menu and it runs
the current version.  Make another update, Ctrl-R, and it runs the previous
version.

Fred


On Tue, September 19, 2017 11:42 am, Gabriel Landini wrote:
On Tuesday, 19 September 2017 16:56:01 BST [hidden email] wrote:
The whole point is that I should not have to restart imagej every time I
need to recompile a Java plugin.  And up to the point that I needed to kill
imagej I did not need to restart.  Help->Refresh Menus does not cause the
newer version of the plugin to be used.

So you mean that the program was modified AND compiled, but the code that
runs
is the old one?
I would check the date of the class file. Maybe the last time it did no
compile? Or maybe there is more than one installation of IJ (I have seen
that
several times, people copying plugins in the plugin folder but which never
appear in the menu... and then realise that there were 2 copies of IJ!

Cheers

Gabriel

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

Date:    Tue, 19 Sep 2017 17:04:13 -0400
From:    anusuya pal <[hidden email]>
Subject: Re: Any suggestions for the estimate of domain size?

Hello,

The image was in tif format, and it can't be opened on many computers. I am
uploading the png format of the same image. And here is the image attached

I need some suggestions about the estimate of the size of the domains.

Thanks in advance
Anu

On Tue, Sep 19, 2017 at 5:00 PM, anusuya pal <[hidden email]> wrote:

Hello,

The image was in tif format, and it can't be opened on many computers. I
am uploading the png format of the same image. And here is the link.:

https://drive.google.com/open?id=0B-zIvUHKCb_zNU1BdUw4NXJmTTA
<https://drive.google.com/open?id=0B-zIvUHKCb_zNXFWRHBEbEpwa1U>

I need some suggestions about the estimate of the size of the domains.

Thanks in advance
Anu

On Tue, Sep 19, 2017 at 4:51 PM, anusuya pal <[hidden email]>
wrote:

Hello,

The image was in tif format, and it can't be opened on many computers. I
am uploading the png format of the same image. And here is the link.:

https://drive.google.com/open?id=0B-zIvUHKCb_zNXFWRHBEbEpwa1U

I need some suggestions about the estimate of the size of the domains.

Thanks in advance
Anu

On Mon, Sep 18, 2017 at 11:08 AM, Dr. Shahzad Ahmad Qureshi <
[hidden email]> wrote:

Image could not open after download. Please send it again.

Dr Shahzad

On Mon, Sep 18, 2017 at 7:12 PM, anusuya pal <[hidden email]>
wrote:

Hello,

I have an image to analyze, and it is very hard to
differentiate/segment. I
have already tried the basic segmentations (Trainable Weka
Segmentation,
Morphological Segmentation, water shedding with BIovoxxel tool etc)
but it
didn't work. I need only the information about the size of the domains
(both big and small). For the convenience, here is the link of the
image
(already converted into 8 bit).

https://drive.google.com/open?id=0B-zIvUHKCb_zdFB1aFBXRlBqcjQ


May I seek your suggestions so that I can estimate the size of the
domains,
without the concern of the hole present inside of the large domain?

Thanks
Anu

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html





--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

Date:    Tue, 19 Sep 2017 17:12:45 -0400
From:    anusuya pal <[hidden email]>
Subject: Any suggestions for the estimate of domain size?

Hello,

I have an image to analyze, and it is very hard to differentiate/segment. I
have already tried all the basic segmentations (Trainable Weka
Segmentation, Morphological Segmentation, water shedding with BIovoxxel
tool etc) but it didn't work. I need only the information about the size of
the domains (both big and small). For the convenience, here is the image
attached(already converted into 8 bit). ​​

May I seek your suggestions so that I can estimate the size of the domains,
without the concern of the hole present inside of the large domain?

I already had this post before but there was a problem of openinf the
image, and so, I posted again with the corrected file format.

Thanks
Anu

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

End of IMAGEJ Digest - 18 Sep 2017 to 19 Sep 2017 - Special issue (#2017-252)
*****************************************************************************


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

Re: Existing efficient macro/plugin for transposing stack/hyperstack

Straatman, Kees (Dr.)
Dear Jeff,

I think you can just change the settings under Image > Properties. This should work for virtual stacks as well.

Best wishes

Kees

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Jeff Hardin
Sent: 19 September 2017 22:30
To: [hidden email]
Subject: Existing efficient macro/plugin for transposing stack/hyperstack

Dear Imagers,
I’m looking for existing code that will take an AxB stack/hyperstack and transpose its entries to a BxA hyperstack. This is useful if a large 4d dataset is already in an A time points of a single focal plane x B focal planes format, but should be in a B focal planes x A time points per focal format.
If the code works on a large stack that can be read in as a Virtual Stack, that would be awesome (my example is a QuickTime movie that has 8100 frames).
Cheers,
Jeff
__________________________
Jeff Hardin
Raymond E. Keller Professor and Chair
Department of Integrative Biology
University of Wisconsin
1117 W. Johnson St.
Madison, WI 53706
voice: (608) 262-9634
fax: (608) 262-7319
email: [hidden email]<mailto:[hidden email]>
web page: http://worms.zoology.wisc.edu

On Sep 19, 2017, at 4:13 PM, IMAGEJ automatic digest system <[hidden email]<mailto:[hidden email]>> wrote:

There are 14 messages totaling 10379 lines in this issue.

Topics in this special issue:

 1. Starting with Fiji
 2. question about plot API
 3. move displayed area to find a marker  4. Announcement: Digital Image Analysis with ImageJ Workshop Nov 7/8/9  5. ImageJ Compile&Run compiles java program in editor but runs from cache.
    How to fix? (7)
 6. Segmentation Editor: Save/Load/Import?
 7. Any suggestions for the estimate of domain size? (2)

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

----------------------------------------------------------------------

Date:    Tue, 19 Sep 2017 04:54:59 +0000
From:    T Purushotham <[hidden email]<mailto:[hidden email]>>
Subject: Starting with Fiji

Respected to all,
Greetings of the day. I have lot of case images of fetal echo with different types like four chamber view, LVOT, RVOT, Three vessel view and Three vessel arch view.Now, I want to develop a macro or algorithm in such a way that, whenever I upload the image  it can automatically identifies the image whether it belongs to which type in above mentioned five cases.
                Can  anyone help me to move forward in this. Also, how far this ImageJ/Fijji useful for me to overcome my problem. Mention any new Machine Learning strategies to solve this.

Thanks and Regards,
T Purushotham,
IIT- Madras.


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

Date:    Mon, 18 Sep 2017 15:53:17 +0200
From:    Michael Schmid <[hidden email]<mailto:[hidden email]>>
Subject: Re: question about plot API

Hi Aryeh,

currently, the ImageJ Plot class only has CONNECTED_CIRCLES, no CONNECTED_TRIANGLES, CONNECTED_CROSSES or so.
I don't think that connected dots would make much sense (the line would hide the dots).  One could think of connected boxes or diamonds [oops, I just see that we even don't have plain diamonds yet!] Beyond ImageJ, I have seen much more plots with connected circles compared to other connected symbols, so I consider this not too bad a choice.
Also, the CONNECTED_CIRCLES are still not as nice as those of some other plotting programs; I think it would be nicer to have the lines end just outside the circles, not go all the way to the centers (if I have much time, maybe I'll change this).  But what we have is better than nothing.


If you want, e.g., connected squares, you could plot the same data set twice, once as squares (BOX), then as a line.

In any case, ImageJ is not a full-fledged plotting program; if you need advanced plots you will still need Gnuplot, Grace, Veusz, etc, or the expensive solution named Origin.


Michael
________________________________________________________________
On 18/09/2017 14:14, Aryeh Weiss wrote:
I have not been able to figure out how to plot connected markers, other than circles. For example:

plt.addPoints(range(1,14), dsum, None, Plot.CONNECTED_CIRCLES, "Total
Area")

adds a trace to plt. However, in another line, I have

plt.addPoints(range(1,14),[x/tmp[0] for x in tmp], None,  i%8 , "Track "+ str(i))

where I use i%8 to cycle through the various markers (CROSS, DOT, TRIANGLE, etc).
and I would like to plot these connected, just like the connected circles, but I cannot find the option to do that.

A second question is how to use the labels that are in the last argument of the addPoints command. I would like to put them in the legend, but I do not see how to recover them in order to add them to the addLegend command.

Thanks in advance for any help on these issues.

--aryeh


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

Date:    Mon, 18 Sep 2017 09:50:20 +0200
From:    Michael Schmid <[hidden email]<mailto:[hidden email]>>
Subject: Re: move displayed area to find a marker

Hi Csaba,

here is a simple macro that takes a point selection with several points and zooms on each of them, one after the other, each time you press the
F8 key.
(you have to install the macro or include it in your StatupMacros)

//global variables, these are remembered var xpoints = newArray(0);  //empty array var ypoints; var pointIndex; var zoom = 18; //actual zoom level will be slightly less, 16x

macro "zoomOnPoints [F8]" {
  if (pointIndex >= xpoints.length) {
    if (selectionType() != 10)
      exit("Multipoint selection needed to start");
    getSelectionCoordinates(xpoints, ypoints);
    pointIndex = 0;
  }
  getLocationAndSize(x, y, width, height); //window size
  x = xpoints[pointIndex];
  y = ypoints[pointIndex];
  w = width/zoom;
  h = height/zoom;
  makeRectangle(x-w/2, y-w/2, w, h);
  run("To Selection");  //zoom to selection
  run("Restore Selection");
  pointIndex++;
}


Michael
________________________________________________________________

On 14/09/2017 09:25, Csaba DÁVID wrote:
Hi,i would like write a macro to find markers (point selection ROIs) that were set earlier on an image. I would like to see them on the zoomed image. Unfortunately, when i click on a ROI in the ROI manager, it can set the layer, but it cannot set the location. The same if I do it with a macro. Is there any command, which moves the displayed are to specified coordinates? It would be extremely useful if i could jump from one ROI location to the next one without zooming out and zooming in again.Csaba

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

Date:    Tue, 19 Sep 2017 10:49:42 -0400
From:    Lai Ding <[hidden email]<mailto:[hidden email]>>
Subject: Announcement: Digital Image Analysis with ImageJ Workshop Nov 7/8/9

Dear Everyone,

The NeuroTechnology Studio at BWH will host a 3-day ImageJ workshop in November 2017. Detailed information is below.

Digital Image Analysis with ImageJ
November 7th – 9th   2017

This intensive 3-day workshop taught by Dr. Lai Ding, Senior Imaging Scientist of the NeuroTechnology Studio(formerly manager of the Harvard NeuroDiscovery Center Enhanced Neuroimaging Core), introduces ImageJ, its basic functions, and its macro programming capabilities. Using real imaging projects, Dr. Ding will demonstrate common image analysis tasks such as basic image processing, stack alignment, cell counting and measurement. Macro writing will be covered to demonstrate how to automate a series of ImageJ commands, to process massive datasets automatically and to store results as desired.

The workshop is broken down into three sessions. Interested participants can sign up for one or more sessions depending on their interest and experience. See tentative schedule below.
If you are interested in this workshop but unable to join this time, please also let us know (email [hidden email]<mailto:[hidden email]>) if you may be able to join the same workshop in the coming months. We MAY host another identical workshop in near future based on the interests shown.
----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- Program Schedule:
Session I (November 7th ) ImageJ for beginners: basic ImageJ functions, measurement, filtering, background subtraction, cell counting, particle analysis, and ethics on image processing.

Session II (November 8th ) Advanced ImageJ: morphology filter, thresholding methods, using ImageJ on FRAP, colocalization analysis and wound assay, working with plugins, designing image analysis protocols.

Session III (November 9th ) ImageJ Macro Programming: introduce ImageJ macro programming language, record image process protocols as macro, batch process multiple images, user interactive features in macro, case study with sample codes. This session is aimed towards the non-programmer, however we do expect the participant to have a basic idea of programming flow control syntax ("for" loop, "if-else" control). The participants are strongly encouraged to go through a brief tutorial on the ImageJ official website before the workshop. http://rsb.info.nih.gov/ij/developer/macro/macros.html

Workshop Location:
L2-025
Countway Library Computer Classroom
Harvard Medical School
10 Shattuck St.
Boston, MA 02115


To register, please complete the online registration form by clicking https://docs.google.com/forms/d/1n3n5tzSR_MM45NqkF1gW4JTa2SfhnaKNEkrry0H5X7o/

For further information please contact: Lai Ding at [hidden email]


Best Regards
Lai Ding

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

Date:    Mon, 18 Sep 2017 23:04:26 -0400
From:    Fred <[hidden email]>
Subject: ImageJ Compile&Run compiles java program in editor but runs from cache. How to fix?

I have been successfully Compile&Run(ing) a Java plugin from the ImageJ editor. At one point the plugin seemed to be in an infinite loop (using massive CPU and not responding to gui interactions). I killed the ImageJ process, and then restarted ImageJ.  Now imagej only runs the version of the program, i.e., class files, that existed when I start imagej.

I can make changes and 'Compile and Run...' .  The java program(s) will compile. Although the program, i.e., class files, that is run is the one that existed when imagej started   I suspect that imagej is caching the class files for some reason, but the cache is prevented from being updated.  Where is this cache or how to get imagej to compile and RUN the program from the editor?

Thanks in advance,

Fred

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

Date:    Tue, 19 Sep 2017 16:33:03 +0100
From:    Gabriel Landini <[hidden email]>
Subject: Re: ImageJ Compile&Run compiles java program in editor but runs from cache. How to fix?

You need to restart ImageJ or run Refresh Menus, (although I seem to remember somebody commenting that restarting is better).
Cheers

Gabriel


On Tuesday, 19 September 2017 04:04:26 BST you wrote:
I have been successfully Compile&Run(ing) a Java plugin from the ImageJ editor. At one point the plugin seemed to be in an infinite loop (using massive CPU and not responding to gui interactions). I killed the ImageJ process, and then restarted ImageJ.  Now imagej only runs the version of the program, i.e., class files, that existed when I start imagej.

I can make changes and 'Compile and Run...' .  The java program(s) will compile. Although the program, i.e., class files, that is run is the one
that existed when imagej started   I suspect that imagej is caching the
class files for some reason, but the cache is prevented from being updated.
Where is this cache or how to get imagej to compile and RUN the program from the editor?

Thanks in advance,

Fred

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

Date:    Tue, 19 Sep 2017 08:27:23 -0700
From:    kscaplen16 <[hidden email]>
Subject: Re: Segmentation Editor: Save/Load/Import?

Hi Daniel and Bene,

I realize this is an old post, but I was wondering if either of you ever got Amira to work with segmentation editor. I am interested in doing exactly what Daniel has proposed: to save and load a current segmentation or even save a finalized segmentation so that I can analyze or reanalyze it at a later time (in 3D ROI manager). Thus far, I am able to save the labels (as a tiff file), which is basically the black screen with my labeled segments, but I am not able to merge it with the actual file that was segmented (the file that has my brain image).

I have downloaded the Amira reader and writer plugins to save my segmentation progress, but Segmentation Editor doesn't seem to recognize the loaded file. Do either of you have any idea as to what I am doing wrong.

Thanks so much in advance for your insight!
Kristin



--
Sent from: http://imagej.1557.x6.nabble.com/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

Date:    Tue, 19 Sep 2017 10:56:01 -0500
From:    Fred Damen <[hidden email]>
Subject: Re: ImageJ Compile&Run compiles java program in editor but runs from cache. How to fix?

The whole point is that I should not have to restart imagej every time I need to recompile a Java plugin.  And up to the point that I needed to kill imagej I did not need to restart.  Help->Refresh Menus does not cause the newer version of the plugin to be used.

Thanks,

Fred

On Tue, September 19, 2017 10:33 am, Gabriel Landini wrote:
You need to restart ImageJ or run Refresh Menus, (although I seem to remember somebody commenting that restarting is better).
Cheers

Gabriel


On Tuesday, 19 September 2017 04:04:26 BST you wrote:
I have been successfully Compile&Run(ing) a Java plugin from the ImageJ editor. At one point the plugin seemed to be in an infinite loop (using massive CPU and not responding to gui interactions). I killed the ImageJ process, and then restarted ImageJ.  Now imagej only runs the version of the program, i.e., class files, that existed when I start imagej.

I can make changes and 'Compile and Run...' .  The java program(s) will compile. Although the program, i.e., class files, that is run is the one
that existed when imagej started   I suspect that imagej is caching the
class files for some reason, but the cache is prevented from being updated.
Where is this cache or how to get imagej to compile and RUN the program from the editor?

Thanks in advance,

Fred

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

Date:    Tue, 19 Sep 2017 17:42:08 +0100
From:    Gabriel Landini <[hidden email]>
Subject: Re: ImageJ Compile&Run compiles java program in editor but runs from cache. How to fix?

On Tuesday, 19 September 2017 16:56:01 BST [hidden email] wrote:
The whole point is that I should not have to restart imagej every time I need to recompile a Java plugin.  And up to the point that I needed to kill imagej I did not need to restart.  Help->Refresh Menus does not cause the newer version of the plugin to be used.

So you mean that the program was modified AND compiled, but the code that runs is the old one?
I would check the date of the class file. Maybe the last time it did no compile? Or maybe there is more than one installation of IJ (I have seen that several times, people copying plugins in the plugin folder but which never appear in the menu... and then realise that there were 2 copies of IJ!

Cheers

Gabriel

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

Date:    Tue, 19 Sep 2017 18:21:40 +0200
From:    Michael Schmid <[hidden email]>
Subject: Re: ImageJ Compile&Run compiles java program in editor but runs from cache. How to fix?

Hi Fred,

in my experience, 'Compile&Run' recompiles source files that are newer than the corresponding .class files. This is true for all classes that are called from the main class (the one you select with 'Compile&Run'), not recursively for others.

So if you have
 My_Plugin, calling
   SubClass1, calling
     SubClass2
and My_Plugin has no reference to SubClass2, then ImageJ won't compile SubClass2, even if SubClass2.java is newer than SubClass2.class.

To make sure, just delete all .class files, then ImageJ will recompile all.


Michael
________________________________________________________________
On 19/09/2017 05:04, Fred wrote:
I have been successfully Compile&Run(ing) a Java plugin from the ImageJ editor. At one point the plugin seemed to be in an infinite loop (using massive CPU and not responding to gui interactions). I killed the ImageJ process, and then restarted ImageJ.  Now imagej only runs the version of the program, i.e., class files, that existed when I start imagej.

I can make changes and 'Compile and Run...' .  The java program(s) will compile. Although the program, i.e., class files, that is run is the one that existed when imagej started   I suspect that imagej is caching the class files for some reason, but the cache is prevented from being updated.  Where is this cache or how to get imagej to compile and RUN the program from the editor?

Thanks in advance,

Fred

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

Date:    Tue, 19 Sep 2017 12:33:07 -0500
From:    Fred Damen <[hidden email]>
Subject: Re: ImageJ Compile&Run compiles java program in editor but runs from cache. How to fix?

Greetings Gabriel,

There is only one copy of ImageJ.  The problem did not exist before I killed imagej while it was stuck. The problem existed after and no other changes have been made, except to the source code of the plugin in question.

The plugin recompiles, timestamps of the class files and java files are when I hit Ctrl-R.  As tests, I inserted a syntax error into the source, hit Ctrl-R, and the error window pops up correctly identifying the syntax error; I erased the .class files while imagej is running and ran the plugin from the Plugins menu and the version that existed when imagej started was run; *without the .class files in the plugins directory*.  This leads me to believe that there is a cache somewhere; which I can not find.

When I start imagej with the .class files in the plugins directory the .class files seem to get placed in some cache somewhere, once they are there they do not get updated.  Running the Help->Refresh Menus with the .class files cached the version that runs is not updated.  As a new test I tried, exiting imagej, erase .class files, start imagej; the plugin does not show up in the Plugins menu; then I update the plugin, i.e., change a string in a IJ.log, Ctrl-R,
Help->Refresh Menus; the plugin now shows up in the Plugins menu and it
Help->runs
the current version.  Make another update, Ctrl-R, and it runs the previous version.

Fred


On Tue, September 19, 2017 11:42 am, Gabriel Landini wrote:
On Tuesday, 19 September 2017 16:56:01 BST [hidden email] wrote:
The whole point is that I should not have to restart imagej every time I need to recompile a Java plugin.  And up to the point that I needed to kill imagej I did not need to restart.  Help->Refresh Menus does not cause the newer version of the plugin to be used.

So you mean that the program was modified AND compiled, but the code that runs is the old one?
I would check the date of the class file. Maybe the last time it did no compile? Or maybe there is more than one installation of IJ (I have seen that several times, people copying plugins in the plugin folder but which never appear in the menu... and then realise that there were 2 copies of IJ!

Cheers

Gabriel

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

Date:    Tue, 19 Sep 2017 15:20:54 -0500
From:    Fred Damen <[hidden email]>
Subject: Re: ImageJ Compile&Run compiles java program in editor but runs from cache. How to fix?

I read a little imagej code and came upon:
/** This version of the constructor is used when ImageJ is launched using Java WebStart. */ public PluginClassLoader(String path, boolean callSuper) { super(new URL[0], Thread.currentThread().getContextClassLoader());
init(path);
}

Which seems like it might be using a cache class loader if 'Java WebStart' is turned on.  How do I tell if it is on and how can it be turned off?

Thanks,

Fred

On Tue, September 19, 2017 12:33 pm, Fred Damen wrote:
Greetings Gabriel,

There is only one copy of ImageJ.  The problem did not exist before I killed imagej while it was stuck. The problem existed after and no other changes have been made, except to the source code of the plugin in question.

The plugin recompiles, timestamps of the class files and java files are when I hit Ctrl-R.  As tests, I inserted a syntax error into the source, hit Ctrl-R, and the error window pops up correctly identifying the syntax error; I erased the .class files while imagej is running and ran the plugin from the Plugins menu and the version that existed when imagej started was run; *without the .class files in the plugins directory*.  This leads me to believe that there is a cache somewhere; which I can not find.

When I start imagej with the .class files in the plugins directory the .class files seem to get placed in some cache somewhere, once they are there they do not get updated.  Running the Help->Refresh Menus with the .class files cached the version that runs is not updated.  As a new test I tried, exiting imagej, erase .class files, start imagej; the plugin does not show up in the Plugins menu; then I update the plugin, i.e., change a string in a IJ.log, Ctrl-R,
Help->Refresh Menus; the plugin now shows up in the Plugins menu and it
Help->runs
the current version.  Make another update, Ctrl-R, and it runs the previous version.

Fred


On Tue, September 19, 2017 11:42 am, Gabriel Landini wrote:
On Tuesday, 19 September 2017 16:56:01 BST [hidden email] wrote:
The whole point is that I should not have to restart imagej every time I need to recompile a Java plugin.  And up to the point that I needed to kill imagej I did not need to restart.  Help->Refresh Menus does not cause the newer version of the plugin to be used.

So you mean that the program was modified AND compiled, but the code that runs is the old one?
I would check the date of the class file. Maybe the last time it did no compile? Or maybe there is more than one installation of IJ (I have seen that several times, people copying plugins in the plugin folder but which never appear in the menu... and then realise that there were 2 copies of IJ!

Cheers

Gabriel

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

Date:    Tue, 19 Sep 2017 17:04:13 -0400
From:    anusuya pal <[hidden email]>
Subject: Re: Any suggestions for the estimate of domain size?

Hello,

The image was in tif format, and it can't be opened on many computers. I am uploading the png format of the same image. And here is the image attached

I need some suggestions about the estimate of the size of the domains.

Thanks in advance
Anu

On Tue, Sep 19, 2017 at 5:00 PM, anusuya pal <[hidden email]> wrote:

Hello,

The image was in tif format, and it can't be opened on many computers. I am uploading the png format of the same image. And here is the link.:

https://drive.google.com/open?id=0B-zIvUHKCb_zNU1BdUw4NXJmTTA
<https://drive.google.com/open?id=0B-zIvUHKCb_zNXFWRHBEbEpwa1U>

I need some suggestions about the estimate of the size of the domains.

Thanks in advance
Anu

On Tue, Sep 19, 2017 at 4:51 PM, anusuya pal <[hidden email]>
wrote:

Hello,

The image was in tif format, and it can't be opened on many computers. I am uploading the png format of the same image. And here is the link.:

https://drive.google.com/open?id=0B-zIvUHKCb_zNXFWRHBEbEpwa1U

I need some suggestions about the estimate of the size of the domains.

Thanks in advance
Anu

On Mon, Sep 18, 2017 at 11:08 AM, Dr. Shahzad Ahmad Qureshi < [hidden email]> wrote:

Image could not open after download. Please send it again.

Dr Shahzad

On Mon, Sep 18, 2017 at 7:12 PM, anusuya pal <[hidden email]>
wrote:

Hello,

I have an image to analyze, and it is very hard to differentiate/segment. I have already tried the basic segmentations (Trainable Weka Segmentation, Morphological Segmentation, water shedding with BIovoxxel tool etc) but it didn't work. I need only the information about the size of the domains (both big and small). For the convenience, here is the link of the image (already converted into 8 bit).

https://drive.google.com/open?id=0B-zIvUHKCb_zdFB1aFBXRlBqcjQ


May I seek your suggestions so that I can estimate the size of the domains, without the concern of the hole present inside of the large domain?

Thanks
Anu

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html





--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

Date:    Tue, 19 Sep 2017 17:12:45 -0400
From:    anusuya pal <[hidden email]>
Subject: Any suggestions for the estimate of domain size?

Hello,

I have an image to analyze, and it is very hard to differentiate/segment. I have already tried all the basic segmentations (Trainable Weka Segmentation, Morphological Segmentation, water shedding with BIovoxxel tool etc) but it didn't work. I need only the information about the size of the domains (both big and small). For the convenience, here is the image attached(already converted into 8 bit). ​​

May I seek your suggestions so that I can estimate the size of the domains, without the concern of the hole present inside of the large domain?

I already had this post before but there was a problem of openinf the image, and so, I posted again with the corrected file format.

Thanks
Anu

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

------------------------------

End of IMAGEJ Digest - 18 Sep 2017 to 19 Sep 2017 - Special issue (#2017-252)
*****************************************************************************


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html