Thank you, everyone who helped with the wand tool solution. Best-
Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory NYU Langone Health, 540 First Avenue, New York, NY 10016 Office: RB (formerly Skirball) 4-102 -- call if door is locked (phone near elevators) Office: 646-501-0567 Cell (voice only, not text): 914-309-3270 [email protected]<mailto:[email protected]> http://nyulmc.org/micros http://microscopynotes.com/ Scheduling the time you want is far more reliable by phone call. Why not provide your phone number? ________________________________ From: Gluender <[email protected]> Sent: Friday, July 4, 2025 6:02 AM To: [email protected] <[email protected]> Subject: Re: help with wand tool [EXTERNAL] Dear Michaels, I've just written off-list to Gabriel with the same conclusion and the attached image. In short, the effect is in fact a consequence of the "Legacy"-scheme. Best Herbie :::::::::::::::::::::::::::::::::::::::::::: Am 04.07.25 um 11:39 schrieb Michael Schmid: > Hi Michael, > > the reason for the problem is the following: > The wand starts from the image center and then goes to the right until > it finds an edge of the thresholded region. In the > 'wand_tool_does_not_work' file it finds an inner hole (one pixel not > thresholded) and thresholds that single pixel. > > You can avoid this by using wand mode '8-connected' instead of the > default (legacy mode). > doWand(getWidth/2, getHeight/2, 0, "8-connected"); > 8-connected mode is also more robust in some other aspects. > Don't care about the tolerance value (3rd argument, here set to 0), it > is ignored for thresholded images. > > > Michael > ________________________________________________________________ > On 03.07.25 18:38, Cammer, Michael wrote: >> >> I posted images at >> https://urldefense.com/v3/__https://microscopynotes.com/temp/wand_tool_works.png__;!!MXfaZl3l!eEzWGltT2QAWZ3YqHOaAtS2wuA6lWAK6E15K1lXDLS9LcSeUpj_i6TryUDDGnptCcsoPN_kApTc7qJkhx8bpzk0$<https://urldefense.com/v3/__https:/microscopynotes.com/temp/wand_tool_works.png__;!!MXfaZl3l!eEzWGltT2QAWZ3YqHOaAtS2wuA6lWAK6E15K1lXDLS9LcSeUpj_i6TryUDDGnptCcsoPN_kApTc7qJkhx8bpzk0$> >> https://urldefense.com/v3/__https://microscopynotes.com/temp/wand_tool_does_not_work.png__;!!MXfaZl3l!eEzWGltT2QAWZ3YqHOaAtS2wuA6lWAK6E15K1lXDLS9LcSeUpj_i6TryUDDGnptCcsoPN_kApTc7qJkhMgLRplk$<https://urldefense.com/v3/__https:/microscopynotes.com/temp/wand_tool_does_not_work.png__;!!MXfaZl3l!eEzWGltT2QAWZ3YqHOaAtS2wuA6lWAK6E15K1lXDLS9LcSeUpj_i6TryUDDGnptCcsoPN_kApTc7qJkhMgLRplk$> >> >> The following code always works when the run("Median...", "radius=2"); >> is run. >> But looking at the image that does not work, I don't see a single >> pixel near getWidth/2, getHeight/2 which does not fall withing the >> threshold range. >> >> Cheers- >> Michael >> >> >> run("Select None"); >> run("8-bit"); >> //run("Median...", "radius=2"); >> setAutoThreshold("Default no-reset"); >> getThreshold(min, max); >> max = max * 1.25; // grab additional periphery which >> may be thin and light >> setThreshold(0, max, "raw"); >> doWand(getWidth/2, getHeight/2); >> run("Set Measurements...", "area display redirect=None decimal=2"); >> run("Measure"); >> print(getTitle + "\t " + getResult("Area") + "\t pixels -- result >> really should be reported as um^2"); >> selectWindow("Log"); >> >> >> >> -----Original Message----- >> From: Gluender <[email protected]> >> Sent: Thursday, July 3, 2025 9:56 AM >> To: [email protected] >> Subject: Re: help with wand tool >> >> [EXTERNAL] >> >> Greetings Michael, >> >> do have images to test? >> >> Best >> >> Herbie >> >> ::::::::::::::::::::::::::::::::::::::::::::: >> Am 03.07.25 um 15:48 schrieb Cammer, Michael: >>> We have images where there is dark object at the center of the field >>> that we want to measure. We are very puzzled because the following >>> code works for some images and not for others. When we manually >>> click using the wand tool, it always works, but this code only works >>> on some images and not others. >>> >>> We are using ImageJ 1.54q14 with java 1.8.0_172. >>> >>> Help would be appreciated. Thank you! >>> >>> // This only reports area. Best fitting ellipse or >>> other morphometrics could be reported. >>> run("Select None"); >>> run("8-bit"); >>> setAutoThreshold("Default no-reset"); >>> getThreshold(min, max); >>> max = max * >>> 1.25; // grab additional >>> periphery which may be thin and light >>> setThreshold(0, max, "raw"); >>> doWand(getWidth/2, getHeight/2); >>> run("Set Measurements...", "area display >>> redirect=None decimal=2"); >>> run("Measure"); >>> print(getTitle + "\t " + getResult("Area") + "\t >>> pixels -- result really should be reported as um^2"); >>> selectWindow("Log"); >>> >>> Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory NYU >>> Langone Health, 540 First Avenue, New York, NY 10016 >>> Office: RB (formerly Skirball) 4-102 -- call if door is locked (phone >>> near elevators) >>> Office: 646-501-0567 Cell (voice only, not text): 914-309-3270 >>> [email protected]<mailto:[email protected]> >>> https://urldefense.com/v3/__http://nyulmc.org/micros__;!!MXfaZl3l!ZXZzBOssOTsy1L_yBR01V3HlavHaYYXIQsn6k_-gmg0nJ1i0f77fj1Ji4siraz3ftIUS7LOL6rDlOCJeaXfxFlo$<https://urldefense.com/v3/__http:/nyulmc.org/micros__;!!MXfaZl3l!ZXZzBOssOTsy1L_yBR01V3HlavHaYYXIQsn6k_-gmg0nJ1i0f77fj1Ji4siraz3ftIUS7LOL6rDlOCJeaXfxFlo$> >>> https://urldefense.com/v3/__http://microscopynotes.com/__;!!MXfaZl3l!ZXZzBOssOTsy1L_yBR01V3HlavHaYYXIQsn6k_-gmg0nJ1i0f77fj1Ji4siraz3ftIUS7LOL6rDlOCJeYipsd6Y$<https://urldefense.com/v3/__http:/microscopynotes.com/__;!!MXfaZl3l!ZXZzBOssOTsy1L_yBR01V3HlavHaYYXIQsn6k_-gmg0nJ1i0f77fj1Ji4siraz3ftIUS7LOL6rDlOCJeYipsd6Y$> >>> >>> Scheduling the time you want is far more reliable by phone call. 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