Micromanager time series issues

[Hani Mahmoud]

Hello all,

I am using Micromanager's (MM) Multi-D Acquisition feature to take a time series of bead images.  I have noticed a discrepancy between the duration I tell MM to take images and the duration MM actually takes.  For example, if I set MM to take 1 image/second and 60 images total, then it indicates (correctly) that the time series should take 1 minute. However, MM often ends up taking the 60 images over a duration of 2 or 3 minutes, rather than 1, as it is supposed to. Clearly this causes my data to become quite inaccurate.

Capturing images at a slower rate did not fix this issue, so I am guessing my camera's limitations are not the problem.

Any suggestions/solutions regarding this issue would be greatly appreciated!

Thank you for your time,

Hani

On Jun 11, 2012, at 9:00 PM, IMAGEJ automatic digest system wrote:

> There are 19 messages totaling 1446 lines in this issue.
>
> Topics of the day:
>
>  1. Fail to modify channel opacity in TrakEM2 (2)
>  2. problem with loading approx. 2GB large data set into FIJI on a 64bit WIN7,
>     24GB RAM machine
>  3. bUnwarpJ: problem saving transformations from macro (3)
>  4. [Janelia Farm] Can ImageJ calculate fiber orientation
>  5. Problem loading > 2GB volume
>  6. Process > Noise > Remove Outliers
>  7. tracking sub-pixel micropillar movements in microscopy
>  8. Mouse Code (5)
>  9. problem reading .ser files.
> 10. running analyze particles on tiff stacks
> 11. Quantifying and Comparing ROIs (2)
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ----------------------------------------------------------------------
>
> Date:    Mon, 11 Jun 2012 03:00:20 -0400
> From:    Federico Luzzati <[hidden email]>
> Subject: Fail to modify channel opacity in TrakEM2
>
> Hi,
> My name is Federico Luzzati and I'm trying to use TrakEM2 to align and reconstruct confocal stacks from serial sections.
>
> I have two main problems:
>
> 1) I'm using RGB images,  but in  the opacity tab I cannot hide channels neither by unchecking the box  or using the slider, I also tryed with RGB stacks, and different files formats (TIF/Jpeg) but nothing changed. I was also wondering whether channels opacity may apply only to the selected layer, or to the entire reconstruction (something that would be really useful for me)
>
> 2) I'd like to perform reconstructions using stacks with multiple channels, (actually "only" four). Any suggestions on how to add a fourth channel? I saw some composite options right clicking in the layer, but could not find them mentioned on the manual.
>
> Thanks a lot for any help
>
> Federico
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> Date:    Mon, 11 Jun 2012 11:14:41 +0200
> From:    Stephan Saalfeld <[hidden email]>
> Subject: Re: Fail to modify channel opacity in TrakEM2
>
> Hi Federico,
>
> TrakEM2's multi-channel support is a bit convoluted, however flexible in
> the way how you can use it.  While it supports RGB images and stacks,
> you have little control there what to do with the channels.  The better
> option is to separate your images stack into single channel images with
> a distinct name (such as "blabla-red.tif") and import them individually
> into the same project.  You can now adjust the channels individually:
>
> Selection->Select all that match...
>
> e.g. Start: 1, End: 1000, Regular expression: .*red.*
>
> Adjust Images->Adjust image filters (selected images)
>
> LUTRed
>
> Properties...
> Composite mode: Add
>
> You'll get it...
>
> The alignment procedures will work on a gray-projection of the
> contrast-overlay setup that you see on screen.  This way you can
> experiment with settings that perform best for alignment (rich texture)
> and later change them to what seems optimal for annotation (clear
> separable signal).
>
> Good luck and best regards,
> Stephan
>
> PS. While the described [procedure should in principle work, I noticed
> that they currently do not because of two bugs in TrakEM2:
>
> http://fiji.sc/cgi-bin/bugzilla/show_bug.cgi?id=435
>
> http://fiji.sc/cgi-bin/bugzilla/show_bug.cgi?id=436
>
> Hope that they turn out to be easy to fix.  Keeping you posted...
>
>
>
>
>
> On Mon, 2012-06-11 at 03:00 -0400, Federico Luzzati wrote:
>> Hi,
>> My name is Federico Luzzati and I'm trying to use TrakEM2 to align and
>> reconstruct confocal stacks from serial sections.
>>
>> I have two main problems:
>>
>> 1) I'm using RGB images, but in the opacity tab I cannot hide channels
>> neither by unchecking the box or using the slider, I also tryed with
>> RGB stacks, and different files formats (TIF/Jpeg) but nothing
>> changed. I was also wondering whether channels opacity may apply only
>> to the selected layer, or to the entire reconstruction (something that
>> would be really useful for me)
>>
>> 2) I'd like to perform reconstructions using stacks with multiple
>> channels, (actually "only" four). Any suggestions on how to add a
>> fourth channel? I saw some composite options right clicking in the
>> layer, but could not find them mentioned on the manual.
>>
>> Thanks a lot for any help
>>
>> Federico
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> Date:    Mon, 11 Jun 2012 13:49:20 +0200
> From:    Michael Schmid <[hidden email]>
> Subject: Re: problem with loading approx. 2GB large data set into FIJI on a 64bit WIN7, 24GB RAM machine
>
> Hi Standa,
>
> looks like a problem of either windows or Java.
>
> Having many hundreds of open windows is probably too much for the Windows operating system. Can you open the images as stack, or in BatchMode (when processing them in a macro), to avoid showing all of them in separate windows?  Anyhow, it won't be of much value to have 800 open windows on the screen at the same time.
> Maybe the WindowTabs might also help (I have never tried it).
>
>
> In case I misunderstood it and you don't have that many open windows, some suggestions to better understand the problem:
>
> - What does Plugins>Utilities>Monitor Memory say? Also clicking on the ImageJ status bar might show you the amount of memory used (as long as it responds).
>
> - What is the size of one of these images in ImageJ (I presume, they are loaded as 16-bit images)? Does the number of open images multiplied by the image size roughly correspond to the memory used by ImageJ and the memory shown in the Task Manager?
> [you would need another byte per pixel for each displayed image]
>
> Maybe you load a smaller dataset that does not freeze the computer for the tests.
>
>
> Michael
> ________________________________________________________________
> On Jun 7, 2012, at 14:22, Standa Vinopal wrote:
>
>> Hi all,
>>
>> I acquire a lot of images on Olympus ScanR, which I need to adjust in ImageJ/Fiji before further analysis. I have a problem with loading a set of 800-900 separate 12-bit tif images, each 2.6 MB big, to FIJI or ImageJ. Loading of images starts normally, but after approx. 500-700 images it is slower and slower and finally it stops and FIJI freezes. When FIJI process is not killed in time, the whole system freezes and needs hard restart. The amount of used RAM by FIJI seen in Windows Task Manager reaches approx. 5,2 GB, Processor load is around 13% and fluctuates a little. There is plenty of system resources unused. It always stops at this value of FIJI-used memory with different data sets excluding the possibility that a wrong image causes the problem. Another interesting feature of this state is that the opened windows start blinking and appearing on the other display (we have two). IT guys do not know what could cause this, video card works normally in other applications and benchmarks. I switched off all the fancy visuals like Aero in Win7, but without an effect.
>>
>> Could you help me to solve that? I know that I could load my images sequentially, but it is not why we bought high-performance computer. ;)
>>
>> Our IT guys made some tests and concluded that computer hardware and software is OK. However, they were not sure about Java settings. Neither do I, because I do not understand it at all.
>>
>> The problem appears both in FIJI 1.46p; Java 1.6.0_24 [64bit] and in ImageJ 1.46m; 1.6.0_20 [64bit]. Memory limit in ImageJ/Fiji is set to 18 GB.
>> Java installed in the computer is 1.7.0_04.
>>
>> Computer:
>> QuadCore Intel core i7 960, 3200 MHz
>> Chipset: Intel Tylersburg x58, Intel Nehalem
>> 24567 MB DDR3-1333 (6x4 GB)
>> Nvidia GeForce GTX 550Ti
>> 180 GB SSD OCZ-VERTEX2 ATA
>> 2TB WDC WD2003FYYs-02W0B0
>> OS: MS Win7 Enterprise, 64bit, version 6.1.7601, SP1; Aero switched off, only Basic Visual mode
>>
>> Thanks in advance for your help!
>>
>> Best wishes,
>>
>> Standa
>>
>> ---------------------------------------------------------------
>> Stanislav Vinopal, Ph.D.
>> Laboratory of Biology of Cytoskeleton
>> Institute of Molecular Genetics ASCR, v.v.i.
>> Videnska 1083, 142 20 Prague 4
>> Czech Republic
>> phone: [phone]
>> e-mail: [hidden email]
>> www.img.cas.cz/dbc
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> Date:    Mon, 11 Jun 2012 07:01:58 -0700
> From:    Tim Grocott <[hidden email]>
> Subject: Re: bUnwarpJ: problem saving transformations from macro
>
> Hi Ignacio,
>
> Thank you very much for your reply, I really appreciate your help!
>
> I can confirm that Fiji is fully up to date (at least that is what the Fiji
> updater tells me). I also checked the ImageJ version from the help menu and
> that says 1.46j (although on loading FIJI the status bar says 1.46p).
>
> As I am using a Mac, FIJI is contained within a package in the applications
> folder. I checked to see if any .txt files were generated within this
> package but none were.  I also did a system-wide search which failed to find
> any .txt file with the appropriate name.
>
> To check if this is a Mac-specific problem I also tried to do this same test
> on a Windows Vista machine. Unfortunately that particular version of FIJI is
> not up to date as I do not have admin access for that machine, (ImageJ
> version is 1.45r). The test fails on the Windows machine (i.e. bUnwarpJ
> generates the .txt file without incident when run from the plugins menu, but
> fails when run from the macro) and this time FIJI gives an error message:
>
> *IOException exceptionjava.io.FileNotFoundException:
> moving_direct_transf.txt (Access is denied)*
>
> Perhaps it is trying to save the .txt file to the FIJI folder as you suggest
> but failing to do so? On the Windows machine this may be because my user
> account does not have write access for C:\Program Files\. I will try again
> on my old Windows XP laptop but ideally I would like to specify a different
> target folder.
>
> I would be very grateful for any other suggestions.
>
> Many thanks again,
> Tim
>
>
> Ignacio Arganda-Carreras wrote
>>
>> Hello Tim,
>>
>> Have you updated Fiji recently? I thought that issue was fixed already. If
>> not, the transformation files are probably stored in your Fiji folder.
>>
>> ignacio
>>
>> On Fri, Jun 8, 2012 at 7:38 AM, Tim Grocott &lt;t.grocott@.ac&gt; wrote:
>>
>>> Hi there,
>>>
>>> I wonder if someone can help. I am attempting to write an ImageJ macro
>>> which
>>> will generate an elastic transformation .txt file by running bUnwarpJ on
>>> two
>>> images.
>>>
>>> I am running an updated Fiji distribution on OS X 10.7.4.
>>>
>>> The problem I have encountered is that no transformation .txt file is
>>> saved
>>> when running bUnwarpJ from a macro. This can be reproduced as follows:
>>>
>>> - Open two images to be registered, e.g. "moving.tif" and "fixed.tif".
>>>
>>> - Click "Plugins > Macros > Record..."
>>>
>>> - Click "Plugins > Registration > bUnwarpJ"
>>>
>>> - In the dialog select the following options:
>>>     Source image = "moving.tif",
>>>     Target image "fixed.tif",
>>>     Registration mode = mono,
>>>     Save transformations = true
>>>
>>> - Click OK to run bUnwarpJ
>>>
>>> - In the "Save_direct_transformation" dialog choose a location for the
>>> transformation .txt file, e.g. the Desktop.
>>>
>>> - The transformation .txt file is saved, in this case to the Desktop as
>>> "moving_direct_transf.txt". So far so good.
>>>
>>> - Delete "moving_direct_transf.txt" from the desktop as we want to see if
>>> a
>>> macro can generate this file.
>>>
>>> - In the Recorder window, click Create to generate a macro for the
>>> recorded
>>> operation. This loads the macro editor with a single line of code as
>>> follows:
>>>
>>> *run("bUnwarpJ", "source_image=moving.tif target_image=fixed.tif
>>> registration=Mono image_subsample_factor=0 initial_deformation=[Very
>>> Coarse]
>>> final_deformation=Fine divergence_weight=0 curl_weight=0
>>> landmark_weight=0
>>> image_weight=1 consistency_weight=10 stop_threshold=0.01
>>> save_transformations
>>>
>>> save_direct_transformation=/Volumes/Data/timothygrocott/Desktop/moving_direct_transf.txt");*
>>>
>>> - Click Run in the macro editor and check to see whether the file
>>> "moving_direct_transf.txt" is saved on the Desktop. In my case no such
>>> file
>>> is generated.
>>>
>>> Is this a known bug? Is there an alternative method for generating a
>>> transformation .txt file? I would be very grateful for any comments or
>>> suggestions.
>>>
>>> Many thanks in advance,
>>> Tim Grocott
>>>
>>> --
>>> View this message in context:
>>> http://imagej.1557.n6.nabble.com/bUnwarpJ-problem-saving-transformations-from-macro-tp4998948.html
>>> Sent from the ImageJ mailing list archive at Nabble.com.
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>
>>
>>
>> --
>> Ignacio Arganda-Carreras, Ph.D.
>> Seung's lab, 46-5065
>> Department of Brain and Cognitive Sciences
>> Massachusetts Institute of Technology
>> 43 Vassar St.
>> Cambridge, MA 02139
>> USA
>>
>> Phone: [phone]
>> Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>
> --
> View this message in context: http://imagej.1557.n6.nabble.com/bUnwarpJ-problem-saving-transformations-from-macro-tp4998948p4998977.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> Date:    Mon, 11 Jun 2012 10:25:45 -0400
> From:    Albert Cardona <[hidden email]>
> Subject: Re: [Janelia Farm] Can ImageJ calculate fiber orientation
>
>> Hi Dr. Cardona,
>>
>> After searching, there are so many websites about your ImageJ tutorials. I'm
>> impressed.
>>
>> My Ph.D. research is about stem cell human mesenchymal cells (hMSC). I've
>> been using DAPI (blue for nucleus) and Rhodamine-Phalloidin (red for F-actin)
>> and I use ImageJ to combine images together to see both nucleus and fibers in
>> one image.
>>
>> To understand in more details, I want to (1) calculate (or count) the number
>> of the nucleus and (2) calculate fiber orientation or how well these
>> microfibers align in one direction compared to others (or in each direction).
>>
>> So, I wondered if I can use ImageJ to do that. If ImageJ can do so, how can I
>> do that?
>>
>> Thank you for your help.
>> Suphannee
>>
>>
>
> Suphannee,
>
> I suggest starting with the ImageJ documentation:
>
> http://rsbweb.nih.gov/ij/docs/index.html
>
> ... and in particular with the user guide:
>
> http://rsbweb.nih.gov/ij/docs/user-guide.pdf
>
>
> Best,
>
> Albert
>
>
>
>
> --
> http://albert.rierol.net
> http://www.ini.uzh.ch/~acardona/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> Date:    Mon, 11 Jun 2012 10:48:10 -0400
> From:    "Rasband, Wayne (NIH/NIMH) [E]" <[hidden email]>
> Subject: Re: Problem loading > 2GB volume
>
> On Jun 9, 2012, at 4:28 PM, Carlos Becker wrote:
>
>> Hello, I am experiencing a problem that was already mentioned here:
>> http://groups.google.com/group/fiji-users/browse_thread/thread/ff62f38b3f2d723d/c6318d467f36e642
>> Is there a possible fix for this issue? I see it happening at the point
>> where Fiji tries to read pixel information beyond the offset 2^31. I have
>> just updated Fiji to the latest version and the problem is still there.
>> In my case the volume is not that big, but pixel type is RGB so the overall
>> size triplicates and this is what makes it unreadable by Fiji.
>>
>> The volume was saved in a .tif file, unsigned char RGB, size 1500x1125x750.
>> Loading shows the "unexpected image offset" at slice 424 which happens to
>> be within the 2^31 boundary.
>
> This bug is fixed in the ImageJ 1.46q daily build, which fixes a bug that caused both File>Open and File>Import>TIFF Virtual Stack to fail when opening >2GB TIFF stacks.
>
> -wayne
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> Date:    Mon, 11 Jun 2012 14:55:12 +0000
> From:    "Cammer, Michael" <[hidden email]>
> Subject: Re: Process > Noise > Remove Outliers
>
> Dear all,
> Apologies for raising this false alarm.  I should have been more careful in my analyses before posting to the group.  The function works fine.
> Regards,
> Michael
>
> -----Original Message-----
>
> On Jun 1, 2012, at 2:40 PM, Cammer, Michael wrote:
>
>> The remove outliers command is great, especially when our images are spatially way oversampled, but I was wondering whether it would be possible to modify it with a hybrid for replacing the pixel.  Right now the pixels are made black when removing high value outliers.  Is there a way we could have a hybrid to replace the center pixel with the average or median of its neighbors?  I could write a macro to do this in a second pass (add 1 to the image and then look for pixels of value 0 to operate on), but it would be much faster to have this included in the command to begin with.
>> Thanks!!
>> ________________________________________________________
>> Michael Cammer, Assistant Research Scientist Skirball Institute of
>> Biomolecular Medicine
>> Lab: [phone]  Cell: [phone]
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> Date:    Mon, 11 Jun 2012 14:57:30 +0000
> From:    "Cammer, Michael" <[hidden email]>
> Subject: tracking sub-pixel micropillar movements in microscopy
>
> Does anybody have experience with imaging the forces of cells as measured by the movements of synthetic micropillars as a cell substrate?  For instance, O du Roure "Force mapping in epithelial cell migration" PNAS 102(7) reports "The resolution of the displacements is of the order of 50 nm..." This is measured by imaging cells by brightfield, phase contrast, or Nomarski and the tops of the micropillars the cells sit on form bright spots.  The underlying spots move as the cell pulls on the substrate.   I was wondering how this can be calculated from images obtained with microscope objectives of  N.A. from 0.80 to 1.40.  For instance, there seem to be MatLab scripts floating around that do this accurately (and, of course, we'd rather use ImageJ).  Any help would be appreciated as we would like to use this method.
>
> Thank you in advance.
>
> Regards,
> Michael
>
> ________________________________________________________
> Michael Cammer, Assistant Research Scientist
> Skirball Institute of Biomolecular Medicine
> Lab: [phone]  Cell: [phone]
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> Date:    Mon, 11 Jun 2012 07:57:54 -0700
> From:    Tim Grocott <[hidden email]>
> Subject: Re: bUnwarpJ: problem saving transformations from macro
>
> Just a quick update,
>
> I downloaded and re-installed FIJI on the Mac (fiji-macosx-20110307.dmg) and
> tried the test before updating (ImageJ version = 1.45b). In this case the
> macro generates a .txt file inside the FIJI package within the Applications
> folder. However, after updating FIJI (ImageJ version = 1.46j [=1.46p in
> status bar]) no .txt file is generated at any location (neither inside the
> FIJI package, nor at the intended location or anywhere else). Hopefully this
> can help to track down the problem.
>
> Many thanks and kind regards,
> Tim
>
>
> Tim Grocott wrote
>>
>> Hi Ignacio,
>>
>> Thank you very much for your reply, I really appreciate your help!
>>
>> I can confirm that Fiji is fully up to date (at least that is what the
>> Fiji updater tells me). I also checked the ImageJ version from the help
>> menu and that says 1.46j (although on loading FIJI the status bar says
>> 1.46p).
>>
>> As I am using a Mac, FIJI is contained within a package in the
>> applications folder. I checked to see if any .txt files were generated
>> within this package but none were.  I also did a system-wide search which
>> failed to find any .txt file with the appropriate name.
>>
>> To check if this is a Mac-specific problem I also tried to do this same
>> test on a Windows Vista machine. Unfortunately that particular version of
>> FIJI is not up to date as I do not have admin access for that machine,
>> (ImageJ version is 1.45r). The test fails on the Windows machine (i.e.
>> bUnwarpJ generates the .txt file without incident when run from the
>> plugins menu, but fails when run from the macro) and this time FIJI gives
>> an error message:
>>
>> *IOException exceptionjava.io.FileNotFoundException:
>> moving_direct_transf.txt (Access is denied)*
>>
>> Perhaps it is trying to save the .txt file to the FIJI folder as you
>> suggest but failing to do so? On the Windows machine this may be because
>> my user account does not have write access for C:\Program Files\. I will
>> try again on my old Windows XP laptop but ideally I would like to specify
>> a different target folder.
>>
>> I would be very grateful for any other suggestions.
>>
>> Many thanks again,
>> Tim
>>
>>
>> Ignacio Arganda-Carreras wrote
>>>
>>> Hello Tim,
>>>
>>> Have you updated Fiji recently? I thought that issue was fixed already.
>>> If
>>> not, the transformation files are probably stored in your Fiji folder.
>>>
>>> ignacio
>>>
>>> On Fri, Jun 8, 2012 at 7:38 AM, Tim Grocott &lt;t.grocott@.ac&gt; wrote:
>>>
>>>> Hi there,
>>>>
>>>> I wonder if someone can help. I am attempting to write an ImageJ macro
>>>> which
>>>> will generate an elastic transformation .txt file by running bUnwarpJ on
>>>> two
>>>> images.
>>>>
>>>> I am running an updated Fiji distribution on OS X 10.7.4.
>>>>
>>>> The problem I have encountered is that no transformation .txt file is
>>>> saved
>>>> when running bUnwarpJ from a macro. This can be reproduced as follows:
>>>>
>>>> - Open two images to be registered, e.g. "moving.tif" and "fixed.tif".
>>>>
>>>> - Click "Plugins > Macros > Record..."
>>>>
>>>> - Click "Plugins > Registration > bUnwarpJ"
>>>>
>>>> - In the dialog select the following options:
>>>>     Source image = "moving.tif",
>>>>     Target image "fixed.tif",
>>>>     Registration mode = mono,
>>>>     Save transformations = true
>>>>
>>>> - Click OK to run bUnwarpJ
>>>>
>>>> - In the "Save_direct_transformation" dialog choose a location for the
>>>> transformation .txt file, e.g. the Desktop.
>>>>
>>>> - The transformation .txt file is saved, in this case to the Desktop as
>>>> "moving_direct_transf.txt". So far so good.
>>>>
>>>> - Delete "moving_direct_transf.txt" from the desktop as we want to see
>>>> if a
>>>> macro can generate this file.
>>>>
>>>> - In the Recorder window, click Create to generate a macro for the
>>>> recorded
>>>> operation. This loads the macro editor with a single line of code as
>>>> follows:
>>>>
>>>> *run("bUnwarpJ", "source_image=moving.tif target_image=fixed.tif
>>>> registration=Mono image_subsample_factor=0 initial_deformation=[Very
>>>> Coarse]
>>>> final_deformation=Fine divergence_weight=0 curl_weight=0
>>>> landmark_weight=0
>>>> image_weight=1 consistency_weight=10 stop_threshold=0.01
>>>> save_transformations
>>>>
>>>> save_direct_transformation=/Volumes/Data/timothygrocott/Desktop/moving_direct_transf.txt");*
>>>>
>>>> - Click Run in the macro editor and check to see whether the file
>>>> "moving_direct_transf.txt" is saved on the Desktop. In my case no such
>>>> file
>>>> is generated.
>>>>
>>>> Is this a known bug? Is there an alternative method for generating a
>>>> transformation .txt file? I would be very grateful for any comments or
>>>> suggestions.
>>>>
>>>> Many thanks in advance,
>>>> Tim Grocott
>>>>
>>>> --
>>>> View this message in context:
>>>> http://imagej.1557.n6.nabble.com/bUnwarpJ-problem-saving-transformations-from-macro-tp4998948.html
>>>> Sent from the ImageJ mailing list archive at Nabble.com.
>>>>
>>>> --
>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>>
>>>
>>>
>>>
>>> --
>>> Ignacio Arganda-Carreras, Ph.D.
>>> Seung's lab, 46-5065
>>> Department of Brain and Cognitive Sciences
>>> Massachusetts Institute of Technology
>>> 43 Vassar St.
>>> Cambridge, MA 02139
>>> USA
>>>
>>> Phone: [phone]
>>> Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>
>
>
> --
> View this message in context: http://imagej.1557.n6.nabble.com/bUnwarpJ-problem-saving-transformations-from-macro-tp4998948p4998980.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> Date:    Mon, 11 Jun 2012 11:28:41 -0400
> From:    Ignacio Arganda-Carreras <[hidden email]>
> Subject: Re: bUnwarpJ: problem saving transformations from macro
>
> Hello Tim,
>
> This is very strange, I tried myself on a Mac and it works for me (the
> files are saved in the Desktop). My status bar says Fiji/ImageJ 1.46p as
> well.
>
> Oh, and it works as well in my Linux machine...
>
> If you want i can send you the JAR file so you can compare with the one you
> have.
>
> ignacio
>
> On Mon, Jun 11, 2012 at 10:57 AM, Tim Grocott <[hidden email]> wrote:
>
>> Just a quick update,
>>
>> I downloaded and re-installed FIJI on the Mac (fiji-macosx-20110307.dmg)
>> and
>> tried the test before updating (ImageJ version = 1.45b). In this case the
>> macro generates a .txt file inside the FIJI package within the Applications
>> folder. However, after updating FIJI (ImageJ version = 1.46j [=1.46p in
>> status bar]) no .txt file is generated at any location (neither inside the
>> FIJI package, nor at the intended location or anywhere else). Hopefully
>> this
>> can help to track down the problem.
>>
>> Many thanks and kind regards,
>> Tim
>>
>>
>> Tim Grocott wrote
>>>
>>> Hi Ignacio,
>>>
>>> Thank you very much for your reply, I really appreciate your help!
>>>
>>> I can confirm that Fiji is fully up to date (at least that is what the
>>> Fiji updater tells me). I also checked the ImageJ version from the help
>>> menu and that says 1.46j (although on loading FIJI the status bar says
>>> 1.46p).
>>>
>>> As I am using a Mac, FIJI is contained within a package in the
>>> applications folder. I checked to see if any .txt files were generated
>>> within this package but none were.  I also did a system-wide search which
>>> failed to find any .txt file with the appropriate name.
>>>
>>> To check if this is a Mac-specific problem I also tried to do this same
>>> test on a Windows Vista machine. Unfortunately that particular version of
>>> FIJI is not up to date as I do not have admin access for that machine,
>>> (ImageJ version is 1.45r). The test fails on the Windows machine (i.e.
>>> bUnwarpJ generates the .txt file without incident when run from the
>>> plugins menu, but fails when run from the macro) and this time FIJI gives
>>> an error message:
>>>
>>> *IOException exceptionjava.io.FileNotFoundException:
>>> moving_direct_transf.txt (Access is denied)*
>>>
>>> Perhaps it is trying to save the .txt file to the FIJI folder as you
>>> suggest but failing to do so? On the Windows machine this may be because
>>> my user account does not have write access for C:\Program Files\. I will
>>> try again on my old Windows XP laptop but ideally I would like to specify
>>> a different target folder.
>>>
>>> I would be very grateful for any other suggestions.
>>>
>>> Many thanks again,
>>> Tim
>>>
>>>
>>> Ignacio Arganda-Carreras wrote
>>>>
>>>> Hello Tim,
>>>>
>>>> Have you updated Fiji recently? I thought that issue was fixed already.
>>>> If
>>>> not, the transformation files are probably stored in your Fiji folder.
>>>>
>>>> ignacio
>>>>
>>>> On Fri, Jun 8, 2012 at 7:38 AM, Tim Grocott &lt;t.grocott@.ac&gt;
>> wrote:
>>>>
>>>>> Hi there,
>>>>>
>>>>> I wonder if someone can help. I am attempting to write an ImageJ macro
>>>>> which
>>>>> will generate an elastic transformation .txt file by running bUnwarpJ
>> on
>>>>> two
>>>>> images.
>>>>>
>>>>> I am running an updated Fiji distribution on OS X 10.7.4.
>>>>>
>>>>> The problem I have encountered is that no transformation .txt file is
>>>>> saved
>>>>> when running bUnwarpJ from a macro. This can be reproduced as follows:
>>>>>
>>>>> - Open two images to be registered, e.g. "moving.tif" and "fixed.tif".
>>>>>
>>>>> - Click "Plugins > Macros > Record..."
>>>>>
>>>>> - Click "Plugins > Registration > bUnwarpJ"
>>>>>
>>>>> - In the dialog select the following options:
>>>>>     Source image = "moving.tif",
>>>>>     Target image "fixed.tif",
>>>>>     Registration mode = mono,
>>>>>     Save transformations = true
>>>>>
>>>>> - Click OK to run bUnwarpJ
>>>>>
>>>>> - In the "Save_direct_transformation" dialog choose a location for the
>>>>> transformation .txt file, e.g. the Desktop.
>>>>>
>>>>> - The transformation .txt file is saved, in this case to the Desktop as
>>>>> "moving_direct_transf.txt". So far so good.
>>>>>
>>>>> - Delete "moving_direct_transf.txt" from the desktop as we want to see
>>>>> if a
>>>>> macro can generate this file.
>>>>>
>>>>> - In the Recorder window, click Create to generate a macro for the
>>>>> recorded
>>>>> operation. This loads the macro editor with a single line of code as
>>>>> follows:
>>>>>
>>>>> *run("bUnwarpJ", "source_image=moving.tif target_image=fixed.tif
>>>>> registration=Mono image_subsample_factor=0 initial_deformation=[Very
>>>>> Coarse]
>>>>> final_deformation=Fine divergence_weight=0 curl_weight=0
>>>>> landmark_weight=0
>>>>> image_weight=1 consistency_weight=10 stop_threshold=0.01
>>>>> save_transformations
>>>>>
>>>>>
>> save_direct_transformation=/Volumes/Data/timothygrocott/Desktop/moving_direct_transf.txt");*
>>>>>
>>>>> - Click Run in the macro editor and check to see whether the file
>>>>> "moving_direct_transf.txt" is saved on the Desktop. In my case no such
>>>>> file
>>>>> is generated.
>>>>>
>>>>> Is this a known bug? Is there an alternative method for generating a
>>>>> transformation .txt file? I would be very grateful for any comments or
>>>>> suggestions.
>>>>>
>>>>> Many thanks in advance,
>>>>> Tim Grocott
>>>>>
>>>>> --
>>>>> View this message in context:
>>>>>
>> http://imagej.1557.n6.nabble.com/bUnwarpJ-problem-saving-transformations-from-macro-tp4998948.html
>>>>> Sent from the ImageJ mailing list archive at Nabble.com.
>>>>>
>>>>> --
>>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Ignacio Arganda-Carreras, Ph.D.
>>>> Seung's lab, 46-5065
>>>> Department of Brain and Cognitive Sciences
>>>> Massachusetts Institute of Technology
>>>> 43 Vassar St.
>>>> Cambridge, MA 02139
>>>> USA
>>>>
>>>> Phone: [phone]
>>>> Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html
>>>>
>>>> --
>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>>
>>>
>>
>>
>> --
>> View this message in context:
>> http://imagej.1557.n6.nabble.com/bUnwarpJ-problem-saving-transformations-from-macro-tp4998948p4998980.html
>> Sent from the ImageJ mailing list archive at Nabble.com.
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>
>
> --
> Ignacio Arganda-Carreras, Ph.D.
> Seung's lab, 46-5065
> Department of Brain and Cognitive Sciences
> Massachusetts Institute of Technology
> 43 Vassar St.
> Cambridge, MA 02139
> USA
>
> Phone: [phone]
> Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> Date:    Mon, 11 Jun 2012 09:01:37 -0700
> From:    David Webster <[hidden email]>
> Subject: Mouse Code
>
> Could someone point me to the ImageJ code use to read mouse cursor
> positions for doing selections.
>
> Thanx - David Webster
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> Date:    Mon, 11 Jun 2012 20:07:57 +0200
> From:    Michael Schmid <[hidden email]>
> Subject: Re: Mouse Code
>
> Hi David,
>
> have a look at ij.gui.ImageCanvas.mousePressed, mouseReleased, mouseMoved.
> These handle the mouse input in images.
>
> These calls are eventually passed to the Roi's mouse handling routines, such as
> ij.gui.Roi.handleMouseDown, handleMouseUp, and ij.gui.PolygonRoi.handleMouseMove
>
> Michael
> ________________________________________________________________
> On Jun 11, 2012, at 18:01, David Webster wrote:
>
>> Could someone point me to the ImageJ code use to read mouse cursor
>> positions for doing selections.
>>
>> Thanx - David Webster
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> Date:    Mon, 11 Jun 2012 14:46:45 -0400
> From:    "Ferez S. Nallaseth" <[hidden email]>
> Subject: Re: Mouse Code
>
> David,
>
> Joel Sheffield of the Department of Biology at Temple University had
> clarified this for us and we have successfully used the application to the
> quantification of many gels. You have to :
>
> 1. open your file (Tiff,Jpeg, etc...)/gel) (to be quantified)through the
> Image J program.
>
> 2. Use the mouse to select the rectangular/circular selection tool.
>
> 3. Outline the band/ROI.
>
> 4. Select the 1st ROI by entering ctrl-1.
>
> 5. Use lateral arrows to move the cursor to the 2nd ROI (restricted to
>   the same plane i.e. left to right but not L->R+Up<->down).
>
> 6. Select the 2nd ROI by entering ctrl-2.
>
> 7. Use lateral arrows to move the cursor to the 3rd ROI.
>
> 8. Select the 3rd ROI by entering ctrl-2 again.
>
> 9. Repeat this for 'n+2' ROIs.
>
> 10. Measure all 'n+2' outlines at once, by entering ctrl-3.
>
> 11. Select peak areas to be quantified (above background) with the
> 'straight,segmented or line tool'.
>
> 12. Quantify each peak with the wand tool from Image J.
> Cautions: (1) size of peak above background, (2) application of the wand
> tool just above demarcating line made by line tool and (3) density of
> pixels beyond opaque affect measurements and increase
> errorrates/artifacts).
>
> 13.First save the results (text and quantified peaks as graphs as jpg
> files)in a folder.
>
> 14. Normalization to a ROI within the linear range of exposure/pixels on a
> given file and repetition of quantifications are necessary.
>
> 15. Plots of the data as Excel graphs can be made by selection, copying
> and pasting of the data from the folder in which they are saved.
>
>
> 16.Detailed instructions are available from the pdf of Image J Manual
> (NIH) (imageJ revised user-guide.8.9.11)
>
> Ferez S. Nallaseth, Ph.D.
>
> Visiting Scientist
>
> Center for Advanced Biotechnology and Medicine
> Rutgers, The State University of New Jersey
> 679 Hoes Lane West
> Piscataway, NJ 08854
>
> Tel: [phone] (M)
> Skype Address: fereznallaseth
> Website:http://sites.google.com/site/nallasethfs
>
>
>
>
>> Could someone point me to the ImageJ code use to read mouse cursor
>> positions for doing selections.
>>
>> Thanx - David Webster
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>
>
>
> Ferez S. Nallaseth, Ph.D.
>
> Visiting Scientist
>
> Center for Advanced Biotechnology and Medicine
> Rutgers, The State University of New Jersey
> 679 Hoes Lane West
> Piscataway, NJ 08854
>
> Tel: [phone] (M)
> Skype Address: fereznallaseth
> Website:http://sites.google.com/site/nallasethfs
>> Could someone point me to the ImageJ code use to read mouse cursor
>> positions for doing selections.
>>
>> Thanx - David Webster
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> Date:    Mon, 11 Jun 2012 14:52:13 -0400
> From:    "Ferez S. Nallaseth" <[hidden email]>
> Subject: Re: Mouse Code
>
> David,
>
> Should it be necessary please feel free to contact me.
>
> Best,
>
> Ferez
>
>
>> Could someone point me to the ImageJ code use to read mouse cursor
>> positions for doing selections.
>>
>> Thanx - David Webster
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>
> Ferez S. Nallaseth, Ph.D.
>
> Visiting Scientist
>
> Center for Advanced Biotechnology and Medicine
> Rutgers, The State University of New Jersey
> 679 Hoes Lane West
> Piscataway, NJ 08854
>
> Tel: [phone] (M)
> Skype Address: fereznallaseth
> Website:http://sites.google.com/site/nallasethfs
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> Date:    Mon, 11 Jun 2012 11:52:18 -0700
> From:    David Webster <[hidden email]>
> Subject: Re: Mouse Code
>
> All,
>
> To clarify, I am interested in finding the code in the ImageJ API that does
> this and that stores(?) a selections coordinates.
>
> David Webster
>
> On Mon, Jun 11, 2012 at 11:46 AM, Ferez S. Nallaseth <
> [hidden email]> wrote:
>
>> David,
>>
>> Joel Sheffield of the Department of Biology at Temple University had
>> clarified this for us and we have successfully used the application to the
>> quantification of many gels. You have to :
>>
>> 1. open your file (Tiff,Jpeg, etc...)/gel) (to be quantified)through the
>> Image J program.
>>
>> 2. Use the mouse to select the rectangular/circular selection tool.
>>
>> 3. Outline the band/ROI.
>>
>> 4. Select the 1st ROI by entering ctrl-1.
>>
>> 5. Use lateral arrows to move the cursor to the 2nd ROI (restricted to
>>  the same plane i.e. left to right but not L->R+Up<->down).
>>
>> 6. Select the 2nd ROI by entering ctrl-2.
>>
>> 7. Use lateral arrows to move the cursor to the 3rd ROI.
>>
>> 8. Select the 3rd ROI by entering ctrl-2 again.
>>
>> 9. Repeat this for 'n+2' ROIs.
>>
>> 10. Measure all 'n+2' outlines at once, by entering ctrl-3.
>>
>> 11. Select peak areas to be quantified (above background) with the
>> 'straight,segmented or line tool'.
>>
>> 12. Quantify each peak with the wand tool from Image J.
>> Cautions: (1) size of peak above background, (2) application of the wand
>> tool just above demarcating line made by line tool and (3) density of
>> pixels beyond opaque affect measurements and increase
>> errorrates/artifacts).
>>
>> 13.First save the results (text and quantified peaks as graphs as jpg
>> files)in a folder.
>>
>> 14. Normalization to a ROI within the linear range of exposure/pixels on a
>> given file and repetition of quantifications are necessary.
>>
>> 15. Plots of the data as Excel graphs can be made by selection, copying
>> and pasting of the data from the folder in which they are saved.
>>
>>
>> 16.Detailed instructions are available from the pdf of Image J Manual
>> (NIH) (imageJ revised user-guide.8.9.11)
>>
>> Ferez S. Nallaseth, Ph.D.
>>
>> Visiting Scientist
>>
>> Center for Advanced Biotechnology and Medicine
>> Rutgers, The State University of New Jersey
>> 679 Hoes Lane West
>> Piscataway, NJ 08854
>>
>> Tel: [phone] (M)
>> Skype Address: fereznallaseth
>> Website:http://sites.google.com/site/nallasethfs
>>
>>
>>
>>
>>> Could someone point me to the ImageJ code use to read mouse cursor
>>> positions for doing selections.
>>>
>>> Thanx - David Webster
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>
>>
>>
>>
>> Ferez S. Nallaseth, Ph.D.
>>
>> Visiting Scientist
>>
>> Center for Advanced Biotechnology and Medicine
>> Rutgers, The State University of New Jersey
>> 679 Hoes Lane West
>> Piscataway, NJ 08854
>>
>> Tel: [phone] (M)
>> Skype Address: fereznallaseth
>> Website:http://sites.google.com/site/nallasethfs
>>> Could someone point me to the ImageJ code use to read mouse cursor
>>> positions for doing selections.
>>>
>>> Thanx - David Webster
>>>
>>> --
>>> 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:    Mon, 11 Jun 2012 22:13:15 +0300
> From:    Aryeh Weiss <[hidden email]>
> Subject: Re: problem reading .ser files.
>
> On 6/11/12 11:15 AM, Kenton Arkill wrote:
>> Hi
>> Not much help, but I use this, and I have seen this message before, but
>> can't remember why.
>> Are you using the plugin direct (ie clicking on it) or by drag and drop?
>> Are you trying to open .ser stacks? Some machines this is possible
>> others it isn't and I don't know why.
>> Try attached macro to get them to .tif (should work in normal imageJ)
>> Regards
>> Kenton
>>
>
> Thank you for your reply. Since the macro depends on the TIA_reader. we
> have the same problem.
>
> However, I discovered something interesting. The TIA_reader can read the
> originally saved .ser file. However, if I copy the file to a second
> file, that second file cannot be read.
>
> This occurred both in Windows and OSX.
>
> This gets curiouser and curiouser.
> --aryeh
>
>> On 10 June 2012 14:09, Aryeh Weiss <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>>    We are trying to read TEM images which were saved in FEI's .ser format.
>>    The TIA_Reader plugin tells us "No Little_Endian Byte ordering"
>>
>>    Is there a way around this?
>>
>>    Thanks in advance.
>>    --aryeh
>>    --
>
>
>
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: [phone]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> Date:    Mon, 11 Jun 2012 16:16:10 -0400
> From:    "Adam T. Greer" <[hidden email]>
> Subject: running analyze particles on tiff stacks
>
> Hello,
>
> I have found ImageJ and especially the "batch statistics" plugin to be
> extremely useful.  However, I would like to take the next step and try
> to create a plugin that would do something similar to 'batch statistics'
> but run the particle analyzer on ~1000 stacks of tiff images within a
> directory.
>
> I have been trying to work off of the java code in 'batch statistics',
> but I have little training in using java for practical purposes (i.e.,
> creating software for some sort of automated analysis).  I used java a
> bit in ecology for agent-based modeling, but this was a different
> application and not well suiting for applying to ImageJ.
>
> I would to know if anyone can offer guidance on creating a plugin that
> does something like the description above.  Do you know of resources
> that can help a novice learn to program for ImageJ plugins or do I just
> need to start at square 1 and learn java programming?  Thanks for any
> help and advice you can give.
>
> --
> Adam T. Greer
> Ph.D Candidate, Graduate Research Assistant
> Marine Biology and Fisheries
> Rosenstiel School of Marine and Atmospheric Science
> 221 South Grosvenor
> Phone: [phone]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> Date:    Mon, 11 Jun 2012 17:13:05 -0400
> From:    Ryan Anderson <[hidden email]>
> Subject: Quantifying and Comparing ROIs
>
> Dear all,
>
> I am currently a graduate student working on my thesis project. Using
> Fiji64, I have been calculating ROIs to quantify changes in the ratio of
> fluorophore intensity for cells' plasma membrane to cytosol staining.
> Specifically, I am trying to look at changes in intensity over time as
> various agents are added to the media. The image sequence data (movie)
> shows clear differences, with changes in intensity between the membrane and
> cytostol. Yet, when I calculate ROIs, the graphs of delta F/F vs time show
> no change. I was hoping to get advice on how to standardize my method, but
> still show an effect. Using the same ROI to calculate the membrane and
> cytosol does not work because the cytosolic changes are much greater than
> can be seen in an ROI that encloses the membrane. Although the peak
> membrane and cytosol intensity seem to equate, one possibility is to make a
> larger ROI for the cytoplasm to better capture the intensity changes. Would
> it be valid then to compare different sized and shaped ROIs for the
> cytoplasm and plasma membrane (keeping the ROIs consistent from cell to
> cell, experiment to experiment)?
>
> Your help is much appreciated.
>
> Sincerely,
>
> Ryan Anderson
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> Date:    Mon, 11 Jun 2012 18:53:27 -0400
> From:    "Joel B. Sheffield" <[hidden email]>
> Subject: Re: Quantifying and Comparing ROIs
>
> It would be helpful if you could post an example, with the ROI's indicated.
>
> On Mon, Jun 11, 2012 at 5:13 PM, Ryan Anderson <[hidden email]> wrote:
>
>> Dear all,
>>
>> I am currently a graduate student working on my thesis project. Using
>> Fiji64, I have been calculating ROIs to quantify changes in the ratio of
>> fluorophore intensity for cells' plasma membrane to cytosol staining.
>> Specifically, I am trying to look at changes in intensity over time as
>> various agents are added to the media. The image sequence data (movie)
>> shows clear differences, with changes in intensity between the membrane and
>> cytostol. Yet, when I calculate ROIs, the graphs of delta F/F vs time show
>> no change. I was hoping to get advice on how to standardize my method, but
>> still show an effect. Using the same ROI to calculate the membrane and
>> cytosol does not work because the cytosolic changes are much greater than
>> can be seen in an ROI that encloses the membrane. Although the peak
>> membrane and cytosol intensity seem to equate, one possibility is to make a
>> larger ROI for the cytoplasm to better capture the intensity changes. Would
>> it be valid then to compare different sized and shaped ROIs for the
>> cytoplasm and plasma membrane (keeping the ROIs consistent from cell to
>> cell, experiment to experiment)?
>>
>> Your help is much appreciated.
>>
>> Sincerely,
>>
>> Ryan Anderson
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>
>
> --
>
>
> Joel B. Sheffield, Ph.D
> Department of Biology
> Temple University
> Philadelphia, PA 19122
> Voice: 215 204 8839
> e-mail: [hidden email]
> URL:  http://astro.temple.edu/~jbs
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> End of IMAGEJ Digest - 10 Jun 2012 to 11 Jun 2012 (#2012-156)
> *************************************************************

--
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[ctrueden]

Hi Hani,


> I am using Micromanager's (MM) Multi-D Acquisition feature to take a time
> series of bead images.


This is the ImageJ list. Perhaps you want to send your question to the
Micro-Manager mailing list instead?
    https://lists.sourceforge.net/lists/listinfo/micro-manager-general

-Curtis


On Tue, Jun 12, 2012 at 1:52 AM, Hani Mahmoud <[hidden email]> wrote:

> Hello all,
>
> I am using Micromanager's (MM) Multi-D Acquisition feature to take a time
> series of bead images.  I have noticed a discrepancy between the duration I
> tell MM to take images and the duration MM actually takes.  For example, if
> I set MM to take 1 image/second and 60 images total, then it indicates
> (correctly) that the time series should take 1 minute. However, MM often
> ends up taking the 60 images over a duration of 2 or 3 minutes, rather than
> 1, as it is supposed to. Clearly this causes my data to become quite
> inaccurate.
>
> Capturing images at a slower rate did not fix this issue, so I am guessing
> my camera's limitations are not the problem.
>
> Any suggestions/solutions regarding this issue would be greatly
> appreciated!
>
> Thank you for your time,
>
> Hani
>

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