Dear all,
I apologise before hand if this has been a topic for conversation previously, but I am a newbie... I am trying to communicate with an automated microscope (Leica DM RXA) through the serial port (Linux and Windows). This consists of basic one line commands with a carriage return and reading from the port. The command will change depending on certain image qualities (ie, auto-focus, etc), so it has to be embedded within a macro I guess. I have read in earlier posts work relating to javacomm, but I have no idea. I am a complete beginner! It would be great if someone could point me in the right direction, preferably with examples... Many thanks, Andy |
Dear Andrew,
at http://mitel.dimi.uniud.it/moss/ijstage.php you can find a package for controlling a Prior Optiscan stage through serial communication, using Javacomm v2.0 (please note the version). It is likely that you can just modify the command strings in the right class to have it function with the Leica microscope, as far as you are interested into stage movements. We are shortly going to release the Marzhauser LSTEP version too, which has some small difference in communication, so if you have problems in trying our package, just ask me. Regards, Vincenzo ------------------------------------------------------------------------ ------------------------ ----------------------------- Vincenzo Della Mea, PhD ------------------------------ ------------ Medical Informatics, Telemedicine and e-health Lab ------------ Dept. of Mathematics and Computer Science - University of Udine, Italy ----------------------- http://www.dimi.uniud.it/dellamea/ ------------------------- ------------------------------ http://mitel.dimi.uniud.it/ -------------------------------- ------------------------------------------------------------------------ ------------------------ |
In reply to this post by Weller Andrew Francis
Hi,
Is there a color correction tool for ImageJ? If not, can someone point me to a source that discusses how to achieve this (a la Photoshop or Gimp). All I have been able to find so far are tutorials on how to use Gimp gray point correction or papers on color constancy. I'm looking for something in between, hopefully. Thanks. Martin |
Martin writes ...
> Is there a color correction tool for ImageJ? If not, can > someone point me to a source that discusses how to achieve > this (a la Photoshop or Gimp). All I have been able to find > so far are tutorials on how to use Gimp gray point correction > or papers on color constancy. I'm looking for something in > between, hopefully. You can use the "gray" eyedropper with PS. It's in the levels and curves dialog boxes. Its use should be described in the PS PDF manual. HTH ... |
Thanks, I'll try and get my hand on a copy (I'm actually using
Gimp). Do you think the manual gives an explanation of how the pixels are processed, or just how to use the eyedropper? I am hoping to reproduce the correction with ImageJ. M At 04:26 PM 1/11/2006, you wrote: > Martin writes ... > > > > Is there a color correction tool for ImageJ? If not, can > > someone point me to a source that discusses how to achieve > > this (a la Photoshop or Gimp). All I have been able to find > > so far are tutorials on how to use Gimp gray point correction > > or papers on color constancy. I'm looking for something in > > between, hopefully. > >You can use the "gray" eyedropper with PS. It's in the levels and curves >dialog boxes. Its use should be described in the PS PDF manual. > >HTH ... |
Martin writes ...
> Thanks, I'll try and get my hand on a copy (I'm actually > using Gimp). Do you think the manual gives an explanation of > how the pixels are processed, or just how to use the > eyedropper? I am hoping to reproduce the correction with ImageJ. I don't think the manual will go into much detail. Keep in mind that PS is a color space savvy software, that is, it would take into account the color space's gamma and therefore the correction is likely too complex for a "users manual". What's entailed is only conceptually understood by myself, which wouldn't include the mathematical details. However, I would also imagine there are plenty of PS users in the scientific community and that you might find some help in the image processing Usenet group, <sci.image.processing>. HTH |
In reply to this post by Martin du Saire
I've done this kind of white balancing manually in ImageJ before. The technique is relatively straightforward and could be turned into a macro if you need to do it often. Here's how I did it.
A patch is gray or white when the values of the 3 color channels (red, green & blue) are equal. So 1st you need to figure out the factors you need to multiply the lower channels by to make them equal to the brighter channel. Here's what I did. Find a part of the image that should be gray. It can be bright, but none of the color values of the pixels should be saturated (i.e., equal to 255) or the ratios of the color channels will not be accurate in this area. To check your selected area for saturation, select the area with the rectangle tool and use the Color Histogram plugin. If a significant fraction of the pixels in any channel is saturated, chose a darker gray area and repeat step 1. If the area is unsaturated, note the mean values of the pixels. You will multiply the channels with the lower means by the number that makes their mean equal to the highest mean. For example, if the red mean is 233.9, the green mean is 207.5 and the blue mean is 176.5, you need to multiply the pixels in the green channel by 233.9 / 207.5 = 1.127 multiply the pixels in the blue channel by 233.9 / 176.5 = 1.325 Now that we have the conversion factors required, we adjust the color intensities. Click outside your selection rectangle to select the whole image. Convert the RGB image into an RGB stack (Menu: Image->Type->RGB Stack) Select a channel in the stack that needs multiplying. Use the menu: Process->Math->Multiply... to multiply the channel by the factor you just calculated. (Answer "No" to the question about processing all 3 slices.) Repeat last 2 steps for the 2nd weak channel. Convert boosted image back to RGB (Menu: Image->Type->RGB Color) That's all. Martin du Saire <[hidden email]> wrote: Thanks, I'll try and get my hand on a copy (I'm actually using Gimp). Do you think the manual gives an explanation of how the pixels are processed, or just how to use the eyedropper? I am hoping to reproduce the correction with ImageJ. M At 04:26 PM 1/11/2006, you wrote: > Martin writes ... > > > > Is there a color correction tool for ImageJ? If not, can > > someone point me to a source that discusses how to achieve > > this (a la Photoshop or Gimp). All I have been able to find > > so far are tutorials on how to use Gimp gray point correction > > or papers on color constancy. I'm looking for something in > > between, hopefully. > >You can use the "gray" eyedropper with PS. It's in the levels and curves >dialog boxes. Its use should be described in the PS PDF manual. > >HTH ... -- Harry Parker Systems Engineer Imaging Systems Division Dialog Semiconductor, Inc. --------------------------------- Yahoo! Photos Ring in the New Year with Photo Calendars. Add photos, events, holidays, whatever. |
Yeah. Now that makes absolute sense. Thanks.
Question: Do you normalize to the highest mean if the patch is dark gray, and the lowest mean if it is light gray? Do you think this kind of color correction can compensate for variability in natural lighting imaging? Thanks again. M At 08:38 PM 1/11/2006, you wrote: >I've done this kind of white balancing manually in ImageJ before. >The technique is relatively straightforward and could be turned into >a macro if you need to do it often. Here's how I did it. > >A patch is gray or white when the values of the 3 color channels >(red, green & blue) are equal. So 1st you need to figure out the >factors you need to multiply the lower channels by to make them >equal to the brighter channel. Here's what I did. |
Free forum by Nabble | Edit this page |