Problems with ImageJ embedded in Micromanager, and Not able to Update the embedded ImageJ

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Problems with ImageJ embedded in Micromanager, and Not able to Update the embedded ImageJ

Geoff Pickford
Hi,

Could someone please help with the following:

PROBLEM 1
I have been using ImageJ’s (Ver 1.51i and r) very useful Plot Profile on a linear series of objects in still images to measure 8-bit gray levels for some time. I recently bought a new camera (AmScope MU503B) so I could do the same analysis on live images using Micromanager (Ver 2.0.0-beta 3 20171122) with its embedded ImageJ (Ver 1.49h).
When using MicroManager and ImageJ’s Plot Profile in ‘live’ mode, I have been using the ImageJ cursor to find the base and the peak grey levels (usually 150 and 130 respectively) of the linear objects. However, when I change the focus or change the selected area, the ‘y’ range changes and causes an immediate loss of 1:1 correlation between the cursor values and the corresponding ‘y’ values. For example, the ‘y’ value may be 150, but the cursor is saying it is say 130. The same with the height of any drawn rectangle on the Profile - e.g. the real height (difference in ‘y’ values) may be 10 gray levels, but the cursor is saying it is 3 gray levels depending upon the windows history since making it ‘live’. I have to quit and restart Plot Profile to correct this problem which is then useless if I make any focus or selected area change.
I have tested stand-alone versions of ImageJ (Ver 1.49v, 1.50i, 1.50r) and ImageJ2 (Ver 2.0.0-rc-43/1/1.51r) on still images and any change of the selected area making a major change in the ‘y’ value of the Plot does NOT create the problems listed above - the ‘y’ values and differences are accurately reflected in the cursor values.
Can anyone please assist me in fixing this problem?

PROBLEM 2
When I try to update ImageJ within MicroManager, using the Help/Update menu, the message comes up ‘Release Notes are not in the expected format’. I have located the ImageJ file in the MicroManager Directory but cannot see how to update it directly. Is anyone please able to sort this out and perhaps give me instructions on how to do it?

PROBLEM 3
I am trying to use a Tucsen ISH500 camera with Micromanager but can see any device configurations to do this, even in the Ver 2.0.0-beta 3 20171122.  Does anyone know how to do this please?
Many thanks


Geoff Pickford


Pickford Resources Pty Ltd
PO Box 618, Wollongong, NSW, 2500
Laboratory Fax:  02 4227 6673.  Mobile:  0417 417 507


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Re: Problems with ImageJ embedded in Micromanager, and Not able to Update the embedded ImageJ

JonD
Administrator
Hi Geoff,


Geoff Pickford wrote

> PROBLEM 1
> I have been using ImageJ’s (Ver 1.51i and r) very useful Plot Profile on a
> linear series of objects in still images to measure 8-bit gray levels for
> some time. I recently bought a new camera (AmScope MU503B) so I could do
> the same analysis on live images using Micromanager (Ver 2.0.0-beta 3
> 20171122) with its embedded ImageJ (Ver 1.49h).
> When using MicroManager and ImageJ’s Plot Profile in ‘live’ mode, I have
> been using the ImageJ cursor to find the base and the peak grey levels
> (usually 150 and 130 respectively) of the linear objects. However, when I
> change the focus or change the selected area, the ‘y’ range changes and
> causes an immediate loss of 1:1 correlation between the cursor values and
> the corresponding ‘y’ values. For example, the ‘y’ value may be 150, but
> the cursor is saying it is say 130. The same with the height of any drawn
> rectangle on the Profile - e.g. the real height (difference in ‘y’ values)
> may be 10 gray levels, but the cursor is saying it is 3 gray levels
> depending upon the windows history since making it ‘live’. I have to quit
> and restart Plot Profile to correct this problem which is then useless if
> I make any focus or selected area change.
> I have tested stand-alone versions of ImageJ (Ver 1.49v, 1.50i, 1.50r) and
> ImageJ2 (Ver 2.0.0-rc-43/1/1.51r) on still images and any change of the
> selected area making a major change in the ‘y’ value of the Plot does NOT
> create the problems listed above - the ‘y’ values and differences are
> accurately reflected in the cursor values.
> Can anyone please assist me in fixing this problem?

Sounds like a bug that has been fixed in recent versions of ImageJ but
persists in the version distributed with MM.  

I understand MM tends to update ImageJ in the distribution infrequently (and
not for several years now) because sometimes that introduces
incompatibilities or interface bugs.  But I have been fine overwriting the
as-distributed ImageJ JAR file with more recent ones for a completely
separate reason, so worth a shot.



Geoff Pickford wrote
> PROBLEM 2
> When I try to update ImageJ within MicroManager, using the Help/Update
> menu, the message comes up ‘Release Notes are not in the expected format’.
> I have located the ImageJ file in the MicroManager Directory but cannot
> see how to update it directly. Is anyone please able to sort this out and
> perhaps give me instructions on how to do it?

Have you tried this:
http://imagej.1557.x6.nabble.com/Update-problem-td5016960.html#a5016968


Geoff Pickford wrote
> PROBLEM 3
> I am trying to use a Tucsen ISH500 camera with Micromanager but can see
> any device configurations to do this, even in the Ver 2.0.0-beta 3
> 20171122.  Does anyone know how to do this please?

Maybe worth contacting Tuscen.  I assume you've searched the mailing list
archives.  Even a separate message to the mailing list with Tuscen in the
subject might get some response.

Jon

--------------------------------------------
Jon Daniels
Applied Scientific Instrumentation
29391 West Enid Rd, Eugene, OR 97402
Phone: (541) 461-8181 x118
--------------------------------------------



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