http://imagej.273.s1.nabble.com/wait-for-a-result-to-appear-tp5017029p5017044.html
Unfortunately deconvolution lab has issues with multi channel images. It
deconvolution, and write a wrapper for multichannel images. I will keep
> Thanks Curtis. The first talk refers to Iterative 3D Deconvolution, which
> was released and last updated in 2005. Multiview deconvolution is for
> light sheet data. Heck I would be using it now if I could get multiview
> reconstruction to work on my home-made instrument. Apparently you need a
> very carefully registered sample holder.
>
> I understand that Ops and GPU deconvolution will be great, eventually.
> Could anyone share their favorite deconvolution plugin that they use right
> now?
>
> I have used commercial packages like Huygens with great success. However
> at the moment I would like to use ImageJ to deconvolve basic widefield
> data for routine tasks. PID is the best of the options I have tested but
> it appears not super compatible with scripting.
>
> All the best,
>
>
> Tim
>
> Timothy Feinstein, Ph.D.
> Research Scientist
> University of Pittsburgh Department of Developmental Biology
>
>
>
>
>
> On 8/17/16, 11:01 AM, "ImageJ Interest Group on behalf of Curtis Rueden"
> <
[hidden email] on behalf of
[hidden email]> wrote:
>
> >Hi Timothy,
> >
> >It is worth noting that Parallel Iterative Deconvolution has not been
> >maintained for many years. I wonder if you have tried any of the more
> >recent deconvolution plugins and algorithms?
> >
> >There were two presentations at the last ImageJ conference:
> >
> >* Brian Northan - Flexible Deconvolution using ImageJ Ops
> > -- video -
> >
https://na01.safelinks.protection.outlook.com/?url=> https%3a%2f%2fvimeo.com
> >%2f140098821&data=01%7c01%7ctnf8%40pitt.edu%
> 7c735fd07cf8494373641d08d3c6b0
> >f63b%7c9ef9f489e0a04eeb87cc3a526112fd0d%7c1&sdata=
> J4MQM6Df0cOfXJP5UEjdpyiw
> >UsSsJbqX6QqXAqqJsDg%3d
> > -- abstract -
> >
https://na01.safelinks.protection.outlook.com/?url=> http%3a%2f%2fimagej.net
> >%2fConference_2015_Program%23Brian_Northan_-_&data=01%
> 7c01%7ctnf8%40pitt.e
> >du%7c735fd07cf8494373641d08d3c6b0f63b%7c9ef9f489e0a04eeb87cc3a526112
> fd0d%7
> >c1&sdata=sZJpBwn6yHYxk3TzzGkWcFCSBIu%2b1jOIWkM7E5eUmQA%3d
> >Flexible_deconvolution_using_ImageJ_Ops
> > -- slides -
> >
https://na01.safelinks.protection.outlook.com/?url=> https%3a%2f%2fimagej.gi
> >thub.io%2fpresentations%2f2015-09-04-&data=01%7c01%7ctnf8%40pitt.edu
> %7c735
> >fd07cf8494373641d08d3c6b0f63b%7c9ef9f489e0a04eeb87cc3a526112
> fd0d%7c1&sdata
> >=lDtyBOntnQcBWB%2bEdh5dH6GueMCEjc2AixX5oSygyzI%3d
> >imagej2-deconvolution/
> >
> >* Benjamin Schmid - Real-time multi-view deconvolution of time-lapse data
> >on the GPU
> > -- video -
> >
https://na01.safelinks.protection.outlook.com/?url=> https%3a%2f%2fvimeo.com
> >%2f140098826&data=01%7c01%7ctnf8%40pitt.edu%
> 7c735fd07cf8494373641d08d3c6b0
> >f63b%7c9ef9f489e0a04eeb87cc3a526112fd0d%7c1&sdata=
> W5yKLyy8h3JfHp4nPZberW7a
> >7gWFAwWfmQdGaWxscuI%3d
> > -- abstract -
> >
https://na01.safelinks.protection.outlook.com/?url=> http%3a%2f%2fimagej.net
> >%2fConference_2015_Program%23&data=01%7c01%7ctnf8%40pitt.edu
> %7c735fd07cf84
> >94373641d08d3c6b0f63b%7c9ef9f489e0a04eeb87cc3a526112
> fd0d%7c1&sdata=vHT%2f7
> >4UKsKVqYwFR21Y2bIkEJB6A5xRzY4reQyaVUCo%3d
> >Benjamin_Schmid_-_Real-time_multi-view_deconvolution_of_
> >time-lapse_data_on_the_GPU
> >
> >See also:
> >
https://na01.safelinks.protection.outlook.com/?url=> http%3a%2f%2fimagej.net
> >%2fDeconvolution&data=01%7c01%7ctnf8%40pitt.edu%
> 7c735fd07cf8494373641d08d3
> >c6b0f63b%7c9ef9f489e0a04eeb87cc3a526112fd0d%7c1&sdata=1qD5mPYlW4Dcu%
> 2fXO2S
> >qzXPOW6k7sW3ghnLcE%2bqSz6gw%3d
> >
> >And improvements to that wiki page are very welcome.
> >
> >Regards,
> >Curtis
> >
> >--
> >Curtis Rueden
> >LOCI software architect -
> >
https://na01.safelinks.protection.outlook.com/?url=http%3a%2f%2floci.wisc> .
> >edu%2fsoftware&data=01%7c01%7ctnf8%40pitt.edu%
> 7c735fd07cf8494373641d08d3c6
> >b0f63b%7c9ef9f489e0a04eeb87cc3a526112fd0d%7c1&sdata=
> Dg44RANnXrWmSyj%2bH5hZ
> >ahzOvervqLECK6%2fzlNQVPGE%3d
> >ImageJ2 lead, Fiji maintainer -
> >
https://na01.safelinks.protection.outlook.com/?url=> http%3a%2f%2fimagej.net
> >%2fUser%3aRueden&data=01%7c01%7ctnf8%40pitt.edu%
> 7c735fd07cf8494373641d08d3
> >c6b0f63b%7c9ef9f489e0a04eeb87cc3a526112fd0d%7c1&sdata=
> w6O2NK61LNyiQffGf9Q9
> >P8wn%2f8DTGSEx4EvGjPWZrMg%3d
> >Did you know ImageJ has a forum?
> >
https://na01.safelinks.protection.outlook.com/?url=> http%3a%2f%2fforum.imag
> >ej.net%2f&data=01%7c01%7ctnf8%40pitt.edu%7c735fd07cf8494373641d08d3c6b0
> f63
> >b%7c9ef9f489e0a04eeb87cc3a526112fd0d%7c1&sdata=ETP6QBbg%
> 2fsFtHR7fc2ZCxJbr5
> >uKj1LX0pL25izztuSI%3d
> >
> >
> >On Wed, Aug 17, 2016 at 9:41 AM, Feinstein, Timothy N <
[hidden email]>
> >wrote:
> >
> >> Thank you Aryeh! I feel silly for missing that basic bit of Java logic.
> >>
> >> Well, that part works now. Now my problem is that any subsequent
> >>command
> >> appears to supercede Parallel Iterative Deconvolution, even 'wait()'.
> >>It
> >> is entirely possible that PID automation only works in isolation and not
> >> inside any more extensive macro. If anyone thinks the problem is
> >> solvable, I pasted my code at the bottom. Note that some long lines of
> >> code will have several paragraph breaks in them when pasting out of an
> >> email.
> >>
> >> All the best,
> >>
> >>
> >> Tim
> >>
> >> Timothy Feinstein, Ph.D.
> >> Research Scientist
> >> University of Pittsburgh Department of Developmental Biology
> >>
> >>
> >>
> >> On 8/16/16, 10:41 PM, "ImageJ Interest Group on behalf of Aryeh Weiss"
> >> <
[hidden email] on behalf of
[hidden email]> wrote:
> >>
> >> >On 17/08/2016 4:34 AM, Feinstein, Timothy N wrote:
> >> >>Hello,
> >> >>
> >> >>I am trying to automate the plugin Parallel Iterative Deconvolution.
> >> >>This plugin does not seem designed for multi-channel images and
> >> >>especially for doing them in batches, so I am trying to patch
> >>together a
> >> >>work-around. The workflow is basically to pre-process for background
> >> >>subtraction, split channels, deconvolve each channel with the
> >> >>appropriate point spread function, delete the originals, merge the
> >> >>results back into one composite and save.
> >> >>
> >> >>This all works fine, except that ImageJ cannot tell that the plugin is
> >> >>still running, so it blazes ahead without the results appearing. I
> >> >>believe in theory I can use the WHILE statement to say something like:
> >> >>
> >> >>while (isOpen("C1-"+Filename[i]+"_WPL_decon") = False) {
> >> >> wait(1000);
> >> >>}
> >> >
> >> >I think you need == , not =.
> >> >Try:
> >> >
> >> >while (isOpen("C1-"+Filename[i]+"_WPL_decon") == False) {
> >> >
> >> >
> >> >>Ideally this should hold the macro in stasis until the deconvolution
> >> >>cycle is finished and a result appears. However ImageJ seems to
> >>think I
> >> >>am missing a parentheses at the equals sign. And I am not sure
> >>whether
> >> >>this strategy would work anyway.
> >> >>
> >> >>Any advice would be appreciated. Best,
> >> >>
> >> >>
> >> >>Tim
> >> >>
> >> >>Timothy Feinstein, Ph.D.
> >> >>
> >> >>--
> >> >>ImageJ mailing list:
> >> >><a href="https://na01.safelinks.protection.outlook.com/?url=http%">https://na01.safelinks.protection.outlook.com/?url=http%
> >> 3a%2f%2fimagej.ni
> >> >>h.gov%2fij%2flist.html&data=01%7c01%7ctnf8%40pitt.edu%7cce
> >> 9b31c0a3ad42887
> >> >>10708d3c649942d%7c9ef9f489e0a04eeb87cc3a526112fd0d%7c1&
> >> sdata=aK0y7w7ZqIAw
> >> >>8CRfzK6chXWzbWzCmjTj6vZqjPDDi6k%3d
> >> >
> >> >
> >> >--
> >> >Aryeh Weiss
> >> >Faculty of Engineering
> >> >Bar Ilan University
> >> >Ramat Gan 52900 Israel
> >> >
> >> >Ph: 972-3-5317638
> >> >FAX: 972-3-7384051
> >> >
> >> >--
> >> >ImageJ mailing list:
> >> ><a href="https://na01.safelinks.protection.outlook.com/?url=http%3a%">https://na01.safelinks.protection.outlook.com/?url=http%3a%
> >> 2f%2fimagej.nih
> >> >.gov%2fij%2flist.html&data=01%7c01%7ctnf8%40pitt.edu%7cce9b
> >> 31c0a3ad4288710
> >> >708d3c649942d%7c9ef9f489e0a04eeb87cc3a526112fd0d%7c1&sdata=
> >> aK0y7w7ZqIAw8CR
> >> >fzK6chXWzbWzCmjTj6vZqjPDDi6k%3d
> >> dir = getDirectory("Input files");
> >> output = getDirectory("Save the results");
> >> filename = getFileList(dir);
> >>
> >> _______________________________________________________
> >>
> >>
> >> dir = getDirectory("Input files");
> >> output = getDirectory("Save the results");
> >> filename = getFileList(dir);
> >>
> >>
> >> pathGreen = File.openDialog("Select the green PSF");
> >> pathRed = File.openDialog("Select the red PSF");
> >> pathFarRed = File.openDialog("Select the far red PSF");
> >>
> >> setBatchMode(false);
> >>
> >> //define the parameters of deconvolution
> >>
> >> function deconvolution() {
> >> pathToBlurredImage = image;
> >> pathToDeblurredImage = deconImage;
> >> pathToPsf = psf;
> >> boundary = "REFLEXIVE"; //available options: REFLEXIVE, PERIODIC,
> >>ZERO
> >> resizing = "AUTO"; // available options: AUTO, MINIMAL,
> >> NEXT_POWER_OF_TWO
> >> output = "SAME_AS_SOURCE"; // available options: SAME_AS_SOURCE,
> >>BYTE,
> >> SHORT, FLOAT
> >> precision = "SINGLE"; //available options: SINGLE, DOUBLE
> >> threshold = "-1"; //if -1, then disabled
> >> maxIters = "10";
> >> nOfThreads = "8";
> >> showIter = "false";
> >> gamma = "0";
> >> filterXY = "1.0";
> >> filterZ = "1.0";
> >> normalize = "false";
> >> logMean = "false";
> >> antiRing = "true";
> >> changeThreshPercent = "0.01";
> >> db = "false";
> >> detectDivergence = "true";
> >>
> >> call("edu.emory.mathcs.restoretools.iterative.ParallelIterat
> >> iveDeconvolutio
> >> n3D.deconvolveWPL", pathToBlurredImage, pathToPsf, pathToDeblurredImage,
> >> boundary, resizing, output, precision, threshold, maxIters, nOfThreads,
> >> showIter, gamma, filterXY, filterZ, normalize, logMean, antiRing,
> >> changeThreshPercent, db, detectDivergence);
> >> }
> >>
> >> //process each file in the input folder
> >>
> >> for (i=0; i<filename.length; i++) {
> >> if(endsWith(filename[i], ".tif")) {
> >> open(dir+filename[i]);
> >> red = "C2-"+filename[i]+"_WPL_decon";
> >> blue = "C3-"+filename[i]+"_WPL_decon";
> >> green = "C1-"+filename[i]+"_WPL_decon";
> >>
> >> //pre-processing for PID: background subtract, add a small saturated
> >>spot
> >> to the first frame in each channel (to get around a quirk in PID's
> >> design), crop (if desired), split channels
> >>
> >> name=getTitle;
> >> run("Subtract Background...", "rolling=50 stack");
> >> run("Canvas Size...", "width=256 height=256 position=Center
> >> zero");
> >> Stack.setSlice(1)
> >> Stack.setChannel(1)
> >> makeRectangle(0, 0, 3, 3);
> >> run("Add...", "value=65535 slice");
> >> Stack.setChannel(2)
> >> makeRectangle(0, 0, 3, 3);
> >> run("Add...", "value=65535 slice");
> >> Stack.setChannel(3)
> >> makeRectangle(0, 0, 3, 3);
> >> run("Add...", "value=65535 slice");
> >> run("Split Channels");
> >>
> >> //deconvolve each channel
> >>
> >> selectWindow("C1-"+filename[i]);
> >> image = getTitle;
> >> deconImage = image+"_WPL_decon";
> >> psf = pathGreen;
> >> deconvolution();
> >> while (isOpen(image+"_WPL_decon") == false) {
> >> wait(1000);
> >> }
> >>
> >> //selectWindow("C1-"+name);
> >> //close;
> >>
> >> selectWindow("C2-"+filename[i]);
> >> image = getTitle;
> >> deconImage = image+"_WPL_decon";
> >> psf = pathRed;
> >> deconvolution();
> >> while (isOpen(image+"_WPL_decon") == false) {
> >> wait(1000);
> >> }
> >>
> >> //selectWindow("C2-"+name);
> >> //close;
> >>
> >> selectWindow("C3-"+filename[i]);
> >> image = getTitle;
> >> deconImage = image+"_WPL_decon";
> >> psf = pathRed;
> >> deconvolution();
> >> while (isOpen(image+"_WPL_decon") == false) {
> >> wait(1000);
> >> }
> >>
> >> //selectWindow("C3-"+name);
> >> //close;
> >>
> >> //reassemble a TIFF from the deconvolved channels and save it
> >>
> >> run("Merge Channels...", "red=["+red+"] green=["+green+"]
> >> blue=["+blue+"] gray=*None* create");
> >> rename(filename[i]+"_deconvolved");
> >> saveName=getTitle;
> >> saveAs("Tiff", output+saveName);
> >> close();
> >>
> >> }
> >> }
> >>
> >>
> >> >
> >>
> >> --
> >> ImageJ mailing list:
> >>
https://na01.safelinks.protection.outlook.com/?url=> http%3a%2f%2fimagej.ni
> >>h.gov%2fij%2flist.html&data=01%7c01%7ctnf8%40pitt.edu%
> 7c735fd07cf84943736
> >>41d08d3c6b0f63b%7c9ef9f489e0a04eeb87cc3a526112
> fd0d%7c1&sdata=1oUyPax9xlcV
> >>h%2fGJABMkuuskiozXfw3AqW0ZJ1BnzkI%3d
> >>
> >
> >--
> >ImageJ mailing list:
> >
https://na01.safelinks.protection.outlook.com/?url=> http%3a%2f%2fimagej.nih
> >.gov%2fij%2flist.html&data=01%7c01%7ctnf8%40pitt.edu%
> 7c735fd07cf8494373641
> >d08d3c6b0f63b%7c9ef9f489e0a04eeb87cc3a526112
> fd0d%7c1&sdata=1oUyPax9xlcVh%2
> >fGJABMkuuskiozXfw3AqW0ZJ1BnzkI%3d
>
> --
> ImageJ mailing list:
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