http://imagej.273.s1.nabble.com/two-color-live-cell-imaging-ratio-data-tp3702347p3702348.html
fluorescence images. So what I did was to subtract the "noisy" channel
>------------------------------
>
>Date: Mon, 26 Jun 2006 10:09:29 -0400
>From: David Knecht <
[hidden email]>
>Subject: two color live cell imaging- ratio data
>
>We are trying to sort out a localization issue for one of our GFP
>probes. The localization is relatively subtle relative to
>cytoplasmic background so we want to be sure it is correct since
>unfused probes are not uniform either. We have co-expressed our GFp-
>fusion and mRFP (cytoplasmic probe) in the same cells to address this
>question.
>1. WHat is the best way to handle this data? It seems this should
>be obvious, but I am struggling with it. FIrst choice is to simply
>make a red-green or cyan-magenta merge, but that requires balancing
>of the two channels and I think it is easy to get fooled trying to
>look for color differences. Second, one could background subtract
>(green-red) but that requires a careful balancing of the two channel
>intensities plus may generate negative numbers. Alternatively, we
>could do a ratio (green/red), but that seems to ask a slightly
>different question. Ratio seems right to me as a way of highlighting
>the relative difference in localization between the two probes.
>2. Assuming one does a ratio (I am using Ratio Plus), the numbers
>come out in the 0-5 range as 32 bit data. How is the result handled
>in ImageJ to generate the kind of color image that I am used to
>seeing from ratio data. Is it a special LUT or do you mathematically
>bring the numbers to a 255 scale and then apply a normal LUT.
>Thanks- Dave
>
>Dr. David Knecht
>Department of Molecular and Cell Biology
>U-3125
>91 N. Eagleville Rd.
>University of Connecticut
>Storrs, CT 06269
>860-486-2200
>860-486-4331 (fax)
>
>------------------------------
>
>Date: Mon, 26 Jun 2006 17:46:50 +0200
>From: Johannes Schindelin <
[hidden email]>
>Subject: Re: image capture
>
>Hi,
>
>On Mon, 26 Jun 2006, Gabriel Landini wrote:
>
> > I thought it would be also nice to make it able to send key presses too,
> > but I am struggling with the last bit: how to convert a string into
> > KeyCode...
>
>I have not tested it, but this snippet could work:
>
>-- snip --
>import java.awt.event.KeyEvent;
>
>[...]
>
>String toSend = "ABC-abc";
>KeyEvent e = new KeyEvent(null,
>for (int i = 0; i < toSend.length(); i++) {
> char c = toSend.charAt(i);
> e.setKeyChar(c);
> int keyCode = e.getKeyCode();
> robot.keyPress(keyCode);
> robot.keyRelease(keyCode);
>}
>-- snap --
>
>Hope this helps!
>Dscho
>
>------------------------------
>
>Date: Mon, 26 Jun 2006 19:37:02 +0200
>From: Albert Cardona <
[hidden email]>
>Subject: Re: image capture
>
>Gabriel,
>
>Yes you can have a plugin running on its own thread that never returns (never
>ends), and either use the Robot class to make clicks (your mouse pointer will
>move too, which is undesirable), or directly execute the button -just capture
>it by exploring down the Container classes. For
>example, from the WindowManager
>get the window of the video, then lists its components, then for each one that
>is a container (JPanel, etc) list its components, et cetera until you find the
>button. Then "doClick()" on the button (if it's a JButton). It all may be
>easier by creating a MouseEvent with the button
>as the object and passing it to
>whatever object is the MouseListener (this is what java does internally
>anyway).
>
>Hope it helps.
>
>Albert
>
>--------------------------------------------------------------------
>This message was sent using Webmail@INI:
https://webmail.ini.ethz.ch>
>------------------------------
>
>Date: Mon, 26 Jun 2006 19:28:42 +0100
>From: Gabriel Landini <
[hidden email]>
>Subject: Re: image capture
>
>On Monday 26 June 2006 18:37, Albert Cardona wrote:
> > Yes you can have a plugin running on its own thread that never returns
> > (never ends), and either use the Robot class to make clicks (your mouse
> > pointer will move too, which is undesirable), or directly execute the
> > button -just capture it by exploring down the Container classes.
>
>Thanks, yes I am trying via the Robot class.
>
> > For
> > example, from the WindowManager get the window of the video, then lists its
> > components, then for each one that is a container (JPanel, etc) list its
> > components, et cetera until you find the button. Then "doClick()" on the
> > button (if it's a JButton). It all may be easier by creating a MouseEvent
> > with the button as the object and passing it to whatever object is the
> > MouseListener (this is what java does internally anyway).
>
>I will have a look at this. I think that the image capture plugin is just a
>wrapper of their image capture which I guess it is written in C or C++ (it
>looks the same, although some functions are greyed out), so that may not
>work.
>Anyway, I will post the robot when it is finished because I think it could be
>quite handy.
>
>Thanks again,
>
>Gabriel
>
>------------------------------
>
>Date: Mon, 26 Jun 2006 13:39:12 -0600
>From: Owen Lockerbie <
[hidden email]>
>Subject: use of imagej to count cells?
>
>does anyone know if image j is able to count positive vs negative =
>stained cells in an immunohistochemical image? - i've attached below a =
>.jpeg image as an example of tumor cells staining positive (brown) vs =
>non-staining cells (blue). it would be great if the program can be used =
>to mark and record # of positive cells vs negative cells instead of =
>laborious and error -prone manual counting
>=20
>in the help menu of the program there doesn't seem to be a counting =
>tool, but maybe i'm just not finding it?
>=20
>any help in using the program for this purpose would be greatly =
>appreciated
>=20
>many thanks!
>=20
>=20
>Owen Lockerbie, PhD
>University of Colorado Cancer Center
>Division of Medical Oncology
>Aurora CO 80010
>Tel 303 724 3875
>email :
[hidden email]
>=20
> =
><
https://webmail.uchsc.edu/exchange/Owen.Lockerbie/Sent%20Items/No%20Subj=>ect-17.EML/Ki67%236-2%20061206.jpg/C58EA28C-18C0-4a97-9AF2-036E93DDAFB3/K=
>i67%236-2%20061206.jpg?attach=3D1>=20
>=20
>=20
>=20
>=20
>=20
>=20
>=20
>=20
>=20
>=20
>=20
>Owen Lockerbie, PhD
>University of Colorado Cancer Center
>Division of Medical Oncology
>Aurora CO 80010
>Tel 303 724 3875
>email :
[hidden email]
>
>________________________________
>
>From: Lockerbie, Owen
>Sent: Mon 6/26/2006 1:34 PM
>To:
[hidden email]
>Subject:=20
>
>
>does anyone know if image j is able to count positive vs negative =
>stained cells in an immunohistochemical image? - i've attached a .jpeg =
>image as an example of tumor cells staining positive (brown) vs =
>non-staining cells (blue). it would be great if the program can be used =
>to mark and record # of positive cells vs negative cells instead of =
>laborious and error -prone manual counting
>=20
>in the help menu of the program there doesn't seem to be a counting =
>tool, but maybe i'm just not finding it?
>=20
>any help in using the program for this purpose would be greatly =
>appreciated
>=20
>many thanks!
>=20
>=20
>Owen Lockerbie, PhD
>University of Colorado Cancer Center
>Division of Medical Oncology
>Aurora CO 80010
>Tel 303 724 3875
>email :
[hidden email]
>
>------------------------------
>
>Date: Mon, 26 Jun 2006 22:21:35 +0200
>From: Vincenzo Della Mea <
[hidden email]>
>Subject: Re: use of imagej to count cells?
>
>If you mean automatic evaluation, ImageJ is not doing that by itself,
>but in principle can be programmed to do it. However, it is a
>difficult task, due to the many variables involved in the staining
>process (I have a student doing a master thesis on that, and I had
>other students in the past, not with ImageJ). A little bit easier
>could be if done on tissue microarrays, because of the possibility of
>including a control core with known positivity and intensity.
>By the way, your attachment cannot be reached without a password.
>Regards,
>Vincenzo Della Mea
>
>Il giorno 26/giu/06, alle ore 21:39, Owen Lockerbie ha scritto:
>
> > does anyone know if image j is able to count positive vs negative
> > stained cells in an immunohistochemical image? - i've attached
> > below a .jpeg image as an example of tumor cells staining positive
> > (brown) vs non-staining cells (blue). it would be great if the
> > program can be used to mark and record # of positive cells vs
> > negative cells instead of laborious and error -prone manual counting
> >
> > in the help menu of the program there doesn't seem to be a counting
> > tool, but maybe i'm just not finding it?
> >
> > any help in using the program for this purpose would be greatly
> > appreciated
>
>* Vincenzo Della Mea
>* Medical Informatics, Telemedicine and Ehealth Lab
>* University od Udine, Italy
>*
http://mitel.dimi.uniud.it/ -
http://www.eslide.net>
>------------------------------
>
>End of IMAGEJ Digest - 25 Jun 2006 to 26 Jun 2006 (#2006-174)
>*************************************************************