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EMBL BioImage Data Analysis



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RT @christlet: After imaging on a LEGO light-sheet with a LEGO pump, you can visualize the data in a LEGO viewer #LEGOallthethings https://…
About 3 hours, 16 mins ago by: Kota Miura (@cmci_)

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RT @jnuneziglesias: STARmap is amazing! But: Groundbreaking paper ✅ Open access ❌ Uses Ilastik ✅ Cites Ilastik ❌ Uses UMAP ✅ Cites UMAP ❌…
About 6 hours, 19 mins ago by: Kota Miura (@cmci_)

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RT @dwaithe: @sossick @BioImagingUK @NEUBIAS_COST @RoyalMicroSoc We did discuss this topic at the last #IAFIGRMS meeting but focused on cos…
About 2 days, 17 hours ago by: Kota Miura (@cmci_)

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RT @HenriquesLab: Coming back to Portugal in a couple of weeks to teach at my original research institute @IGCiencia. We'll be giving the #…
About 3 days, 1 hour ago by: Kota Miura (@cmci_)

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RT @bxv_cell: CDeep3M - Plug-and-Play cloud based deep learning for image segmentation of light, electron and X-ray microscopy
About 3 days, 1 hour ago by: Kota Miura (@cmci_)

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RT @robustgar: New post: Small n correlations + p values = disaster
About 3 days, 1 hour ago by: Kota Miura (@cmci_)


QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ Nature Methods 7, 339 - 340 (2010) doi:10.1038/nmeth0510-339

PALM and STORM reconstruction algorithms usually rely on 'fitting' Gaussian kernels to detected diffraction-limited spots. Although they permit high-accuracy localizations, these iterative methods can require up to several hours of processing time. We have developed a high-speed reconstruction algorithm that uses the classical Högbom 'CLEAN' method8 for spot finding, followed by a modified center of mass algorithm to compute the spot position and parameters defining spot shape along the horizontal axes.

I have not yet tried this, but seems to be very usable also for simple cases that needs to find spots. Plugin could be downloaded from


24 -12 =​ ?
blogtng/2010-05-19/quickpalm.txt · Last modified: 2016/05/24 05:46 (external edit)