DeconvolutionLab Batch Processing
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Hello
I wish to use DeConvolutionLab to perform batch processing on a number of .tiff stacks. I can choose the Input and Output folders without a problem. When I hit RUN it will show me the Initial input files and the new output file names. However, it asks me for PSF file. When I do them individually, I use the same file as both input and output. But am not sure how to do this for batch? Any help appreciated. I have 100s of files to process ! :) |
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Hi
Do you have the PSF image open?? I've done this before and I needed to open the PSF image, go to the PSF option, then select "Flip PSF Quadrants" (if the PSF is centered). After that select the input and output folders. It should then process all the files using the same PSF. Brian On Thu, Sep 19, 2013 at 5:52 PM, mehulmvora <[hidden email]> wrote: > Hello > > I wish to use DeConvolutionLab to perform batch processing on a number of > .tiff stacks. > > I can choose the Input and Output folders without a problem. When I hit RUN > it will show me the Initial input files and the new output file names. > > However, it asks me for PSF file. > > When I do them individually, I use the same file as both input and output. > But am not sure how to do this for batch? > > Any help appreciated. I have 100s of files to process ! :) > > > > -- > View this message in context: > http://imagej.1557.x6.nabble.com/DeconvolutionLab-Batch-Processing-tp5004865.html > Sent from the ImageJ mailing list archive at Nabble.com. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: DeconvolutionLab Batch Processing
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Hi Brian Thank you for your reply. I'm a complete newbie to deconvolution and confocal microscopy. I don't have individual PSF files for each of the images - isn't that what's required? Each image is different from the rest (but they were taken at the same time with the same scope and settings). Will one PSF file work for them all? I thought that each image will have it's own psf? Thank you! On Fri, Sep 20, 2013 at 12:52 PM, bnorthan [via ImageJ] <[hidden email]> wrote: Hi |
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One PSF file should work for them all assuming similar acquisition
conditions. The PSF is actually a little bit different for each location within one image. That is because the PSF is determined by the path the light takes through the sample, and the refractive index of the sample (and for a real sample the RI will be different throughout). Assuming one PSF for the image is a "approximation" that is used for most deconvolution algorithms (unless you get into algorithms that use special schemes to subdivide the image). Likewise assuming one PSF for the entire set is fine assuming all images were taken under similar settings. How are you getting the PSF?? A bead image?? On Fri, Sep 20, 2013 at 1:04 PM, mehulmvora <[hidden email]> wrote: > Hi Brian > > Thank you for your reply. I'm a complete newbie to deconvolution and > confocal microscopy. > > I don't have individual PSF files for each of the images - isn't that > what's required? Each image is different from the rest (but they were taken > at the same time with the same scope and settings). Will one PSF file work > for them all? I thought that each image will have it's own psf? > > Thank you! > > > On Fri, Sep 20, 2013 at 12:52 PM, bnorthan [via ImageJ] < > [hidden email]> wrote: > > > Hi > > > > Do you have the PSF image open?? I've done this before and I needed to > > open > > the PSF image, go to the PSF option, then select "Flip PSF Quadrants" (if > > the PSF is centered). After that select the input and output folders. > > > > It should then process all the files using the same PSF. > > > > Brian > > > > > > On Thu, Sep 19, 2013 at 5:52 PM, mehulmvora <[hidden email]< > http://user/SendEmail.jtp?type=node&node=5004880&i=0>> > > wrote: > > > > > Hello > > > > > > I wish to use DeConvolutionLab to perform batch processing on a number > > of > > > .tiff stacks. > > > > > > I can choose the Input and Output folders without a problem. When I hit > > RUN > > > it will show me the Initial input files and the new output file names. > > > > > > However, it asks me for PSF file. > > > > > > When I do them individually, I use the same file as both input and > > output. > > > But am not sure how to do this for batch? > > > > > > Any help appreciated. I have 100s of files to process ! :) > > > > > > > > > > > > -- > > > View this message in context: > > > > > > http://imagej.1557.x6.nabble.com/DeconvolutionLab-Batch-Processing-tp5004865.html > > > Sent from the ImageJ mailing list archive at Nabble.com. > > > > > > -- > > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > > ------------------------------ > > If you reply to this email, your message will be added to the discussion > > below: > > > > > http://imagej.1557.x6.nabble.com/DeconvolutionLab-Batch-Processing-tp5004865p5004880.html > > To unsubscribe from DeconvolutionLab Batch Processing, click here< > > > > . > > NAML< > http://imagej.1557.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml > > > > > > > > > -- > View this message in context: > http://imagej.1557.x6.nabble.com/DeconvolutionLab-Batch-Processing-tp5004865p5004882.html > Sent from the ImageJ mailing list archive at Nabble.com. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: DeconvolutionLab Batch Processing
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Hello - thanks again for the reply. I'm generating a PSF using the Diffraction PSF 3d plugin. No beads unfortunately On Fri, Sep 20, 2013 at 2:48 PM, bnorthan [via ImageJ] <[hidden email]> wrote: One PSF file should work for them all assuming similar acquisition |
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Are your original images wide field or confocal??
If confocal do you have a way to generate a confocal psf with ImageJ? That is something I'm curious about myself. I've looked at "Diffraction PSF 3D" and "PSF Generator" (from BIG lab) but couldn't figure out how to do it. Maybe I'm overlooking an option?? On Fri, Sep 20, 2013 at 3:25 PM, mehulmvora <[hidden email]> wrote: > Hello - thanks again for the reply. I'm generating a PSF using the > Diffraction PSF 3d plugin. No beads unfortunately > > > On Fri, Sep 20, 2013 at 2:48 PM, bnorthan [via ImageJ] < > [hidden email]> wrote: > > > One PSF file should work for them all assuming similar acquisition > > conditions. > > > > The PSF is actually a little bit different for each location within one > > image. That is because the PSF is determined by the path the light takes > > through the sample, and the refractive index of the sample (and for a > real > > sample the RI will be different throughout). > > > > Assuming one PSF for the image is a "approximation" that is used for most > > deconvolution algorithms (unless you get into algorithms that use special > > schemes to subdivide the image). Likewise assuming one PSF for the > entire > > set is fine assuming all images were taken under similar settings. > > > > How are you getting the PSF?? A bead image?? > > > > > > On Fri, Sep 20, 2013 at 1:04 PM, mehulmvora <[hidden email]< > http://user/SendEmail.jtp?type=node&node=5004883&i=0>> > > wrote: > > > > > Hi Brian > > > > > > Thank you for your reply. I'm a complete newbie to deconvolution and > > > confocal microscopy. > > > > > > I don't have individual PSF files for each of the images - isn't that > > > what's required? Each image is different from the rest (but they were > > taken > > > at the same time with the same scope and settings). Will one PSF file > > work > > > for them all? I thought that each image will have it's own psf? > > > > > > Thank you! > > > > > > > > > On Fri, Sep 20, 2013 at 12:52 PM, bnorthan [via ImageJ] < > > > [hidden email] <http://user/SendEmail.jtp?type=node&node=5004883&i=1>> > > wrote: > > > > > > > Hi > > > > > > > > Do you have the PSF image open?? I've done this before and I needed > to > > > > open > > > > the PSF image, go to the PSF option, then select "Flip PSF Quadrants" > > (if > > > > the PSF is centered). After that select the input and output > folders. > > > > > > > > It should then process all the files using the same PSF. > > > > > > > > Brian > > > > > > > > > > > > On Thu, Sep 19, 2013 at 5:52 PM, mehulmvora <[hidden email]< > > > http://user/SendEmail.jtp?type=node&node=5004880&i=0>> > > > > wrote: > > > > > > > > > Hello > > > > > > > > > > I wish to use DeConvolutionLab to perform batch processing on a > > number > > > > of > > > > > .tiff stacks. > > > > > > > > > > I can choose the Input and Output folders without a problem. When I > > hit > > > > RUN > > > > > it will show me the Initial input files and the new output file > > names. > > > > > > > > > > However, it asks me for PSF file. > > > > > > > > > > When I do them individually, I use the same file as both input and > > > > output. > > > > > But am not sure how to do this for batch? > > > > > > > > > > Any help appreciated. I have 100s of files to process ! :) > > > > > > > > > > > > > > > > > > > > -- > > > > > View this message in context: > > > > > > > > > > > > > > > http://imagej.1557.x6.nabble.com/DeconvolutionLab-Batch-Processing-tp5004865.html > > > > > Sent from the ImageJ mailing list archive at Nabble.com. > > > > > > > > > > -- > > > > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > > > > > > > > > -- > > > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > > > > > > > > ------------------------------ > > > > If you reply to this email, your message will be added to the > > discussion > > > > below: > > > > > > > > > > > > > > http://imagej.1557.x6.nabble.com/DeconvolutionLab-Batch-Processing-tp5004865p5004880.html > > > > To unsubscribe from DeconvolutionLab Batch Processing, click here< > > > > > > > > > > . > > > > NAML< > > > > > > http://imagej.1557.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > View this message in context: > > > > > > http://imagej.1557.x6.nabble.com/DeconvolutionLab-Batch-Processing-tp5004865p5004882.html > > > > > Sent from the ImageJ mailing list archive at Nabble.com. > > > > > > -- > > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > > ------------------------------ > > If you reply to this email, your message will be added to the discussion > > below: > > > > > http://imagej.1557.x6.nabble.com/DeconvolutionLab-Batch-Processing-tp5004865p5004883.html > > To unsubscribe from DeconvolutionLab Batch Processing, click here< > > > > . > > NAML< > http://imagej.1557.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml > > > > > > > > > -- > View this message in context: > http://imagej.1557.x6.nabble.com/DeconvolutionLab-Batch-Processing-tp5004865p5004884.html > Sent from the ImageJ mailing list archive at Nabble.com. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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