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NoPhotonLeftBehind
United States
Приєднався 26 чер 2015
Bio image analysis tutorials, focused on open source software and models.
µTalks v2 #6 - Figures, Methods and Publications
µTalks v2 #6 - Figures, Methods and Publications
Переглядів: 95
Відео
µTalks v2 #4 - Acquisition Optimization
Переглядів 1133 роки тому
µTalks v2 #4 - Acquisition Optimization
µTalks v2 #5 - Data Analysis
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Part #5 in our revamped series on fluorescence microscopy: Data Analysis. Covers overview of data analysis concepts. Please reach out to the ICI core as early as possible in your quantitative experiments.
µTalks v2 #1 - Intro to Fluorescence Labeling
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First part in our revamped series on fluorescence microscopy: Intro to Fluorescence Labeling. Covers overview of immunofluorescence, some fluorescence protein information, and details of one of our mantras: Know Your Spectra
µTalks v2 #2 - Advanced labeling Protocols
Переглядів 3623 роки тому
Second part in our revamped series on fluorescence microscopy: Advanced labeling Protocols. Covers a more detailed dive into protocols relating to chemical probes, fluorescence proteins and immunofluorescence.
Fiji, ilastik, Cellprofiler - Workflow Series Part 2
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Basic steps to train and apply a pixel classification machine learning model in ilastik
Fiji, ilastik, Cellprofiler - Workflow Series Part 1b
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Ad hoc workflow on how to make a macro from scratch, including some resources and misc tips
Fiji, ilastik, Cellprofiler - Workflow Series Part 1a
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Fiji macro to export single channel tifs
Fiji, ilastik, Cellprofiler - Workflow Series Part 0
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Intro into the workflow series using a Fiji macro to export tif files, followed by a basic annotated ilastik machine learning model to identify cells, and then an analysis pipeline in Cellprofiler to quantify and export the results. We'll also touch on how to work with Cellprofiler exports using Power BI and/or Pivot Tables in Excel
Emory ICI Abberior 3D STED Webinar
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Overviews Emory's Integrated Cellular Imaging Core followed by fast paced webinar on all the features and capabilities of our Abberior easy3D Facility Line STED microscope.
Fiji Is Just ImageJ - ome.tif - Part 4 - Tidy Macro
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Macro available here: www.cores.emory.edu/ici/resources/plugins.html
Fiji Is Just ImageJ - ome.tif - Part 3 - Macro
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Macro available here: www.cores.emory.edu/ici/resources/plugins.html
Fiji Is Just ImageJ - ome.tif - Part 2 - Metadata
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Fiji Is Just ImageJ - ome.tif - Part 2 - Metadata
Fiji Is Just ImageJ - ome.tif - Part 1 - Simple Export
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Fiji Is Just ImageJ - ome.tif - Part 1 - Simple Export
Fiji Is Just ImageJ - Batch Convert to Tif, Part 2
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Fiji Is Just ImageJ - Batch Convert to Tif, Part 2
Fiji Is Just ImageJ - Batch Convert to Tif, Part 1
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Fiji Is Just ImageJ - Batch Convert to Tif, Part 1
Imaris - Spots for Mitochondria Estimates
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Imaris - Spots for Mitochondria Estimates
Fiji Is Just ImageJ - Extended Orthogonal Views and Reslice
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Fiji Is Just ImageJ - Extended Orthogonal Views and Reslice
Fiji Is Just ImageJ - Orthogonal Views
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Fiji Is Just ImageJ - Orthogonal Views
Imaris - Orthogonal Views & Clipping
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Imaris - Orthogonal Views & Clipping
Imaris - MIP, Blend & Normal Display Modes
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Imaris - MIP, Blend & Normal Display Modes
Fiji Is Just ImageJ - Export Data Tiff - Volocity .mvd2
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Fiji Is Just ImageJ - Export Data Tiff - Volocity .mvd2
Fiji Is Just ImageJ - Save As Movie - Volocity .mvd2 Files
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Fiji Is Just ImageJ - Save As Movie - Volocity .mvd2 Files
Thank you
Thankyou this was very helpful
Hey, is there a way you can convert .tiff to .czi??? Really need help😭
Hello, thank you for this very useful tutorial. I have no experience with JAVA's scripts. I have a question: I do not have any ".format" at the end of my images (dicom images), how should I proceed with the "replace" command? If I just delete ".oib", it gives me error but I do not know how to address that error. Thank you.
Hello, this is a great video! What does it mean the + signs before and after the pStr? Thank you.
Hi there, Many thanks for your videos. I was wondering if there is a way to measure length of particles in one area rather than just the area of particles? Many thanks in advance
This is brilliantly done- thank you so much for posting!
Quite helpful video :)
This video is so helpful!! Thank you!
your nuclear stain should be crystal clear. The non-nuclear debris is mycoplasma in your sample....
I'm using Fiji to merge my cell images, so after I have recorded my macros the program won't run stating there's no "file name " do I have to rename something or change the code somewhere ?
I have a single plane image, I have 4 channels. I tried the following: title = getTitle(); run("Split Channels"); one = "C1-" + title; two = "C2-" + title; three = "C3-" + title; four = "C4-" + title; run("Merge Channels...", "c1=["+one+"] c2=["+two+"] c3=["+three+"] c4=["+four+"] create"); run("RGB Color"); selectWindow(title) close() selectWindow(title + " (RGB)") It works as a macro on open files but not in batch mode as at 3:28. Can anyone help me to troubleshoot this? Thanks.
Thanks a lot, I wasn't aware of how to save the images with the yellow lines! thanks again
Hello, when I plan to create surface in Imaris and draw a circle on images, it always indicate that"Could not create a surface with current defined resolution. Please try to create a surface again after manually defining a higher resolution on Board Tab", but when I adjust resolution, I still can not work, would you please tell me what should I do?
voi.fyi delightful
I want to clarify that for staining the secondary, the slide mentions 1-2 hours but I spoke 1-2 minutes. The slide has the correct duration. Happy Staining :)
This is great! Thanks so much for posting this.
Great Video. I have a question. ¿How can I create a macros with a square form?
Toda Raba 🙏 thanks
Hi, I would like to remove the Grid from the Imaris Stitched image using ImageJ. Could please create video on this?
Hi! Great video. When you are analyzing a set of images and want to compare spot counts, this value below the filter tab, which is the bottom left diagram's threshold - would you keep it as generated automatically or adjust and use the same manual value for all the images? Hope it made sense)) Thanks!!
Thanks, how would you then assign that macro to a hotkey or shortcut?
Would Weka Segmentation be a substitute for the llastik model?
Yes, you'd be able to use Weka, and that way you could keep everything in Fiji and potentially write a macro that there that handles the whole process, including saving the results.
Another way, if you want to keep things in Fiji, is to train the model in ilastik, and then use the ilastik plugin in Fiji to apply that model from a macro. You have to spend time training either direction, and it's whatever you're more familiar with.
what video card do you use?
I think this was on a 1080 Ti, but we had a 1070 Ti and it does really well. We also have used quadro M series, but they're not worth the money unless you absolutely need the VRAM.
Great video!!
Hi when trying to save a tiff time lapse as a movie, I get this error "higher dimension stack not supported please reduce depth or time". What does this mean and how can I overcome this? Thanks in advance!
Sorry for the delay. Not sure what might be going on. Please email nophotonleftbehind@gmail.com and share the data and I'm happy to take a look :)
thanks! was this image deconvolved before doing the isospot analysis or is that not recommended?
Decon is fine as long as it follows the rules. If not you'll end up with artifacts and you might end up chasing ghosts. You need to have a well matched refractive index, you'll need a relatively thin sample (not something I'd advise for tissue if you want to be strictly quantitative), nice specific labeling, and good signal to noise.
Hi, thank you for your video. I noticed that after Re-Slicing from Left you would need to Flip your new stack Horizontally in order to get the same orientation as in the Orthogonal View in the YZ plane. Do you know if there is a command to get the same in orientation automatically without needing the "Flip Horizontal" step after the reslicing? Thanks!!
I'm not sure I understand exactly what you mean, but if you check "Rotate 90 degree" it looks to match the orthogonal view.
Thanks for the informative video! Is there a way to add text, such as labels, during the animation?
Likely not in the way you'd like. Imaris does have annotation, but it's kinda limited. I'll see what I can do to add those details when I finally find time to revisit.
I do not have the "close" on the operation to perform, why is that? My Cell Profiler is 3.1.9
Not sure. I'm gonna revisit a similar pipeline using CP 4 soon, and maybe that will be of help. You'll be able to get direct help from the devs if you post on forum.image.sc/
@@nophotonleftbehind Appreciate it, thank you!
Hi, thank you for your generous aid I am a beginner, I would like to take your advice about the type of microscopy and camera I should use in H &E-stained sections and how I could use a statistical analysis to detect a certain effect a in the treated tissue sections cytoplasm or nuclei. And is it applicable on the ultrastructuer by EM? . And I would like to have further communication with you. Regards
Hi Wafaa, thanks for the input. I'm not sure these UA-cams are directly for that purpose, but maybe an upcoming series on ilastik might help with some of your analyses. Subscribe to get updates of that soon. Also, you should search, join, and post on forum.image.sc/ for things along those lines. You'll find a huge community of knowledgeable and helpful people :)
Thank for the video ! Do I need to create the same macro (SetChn.ijm) ? Did not find it on the imageJ website
Not sure about SetChn.ijm... Are you using ImageJ or Fiji?
I just finished your tutorial series, thank you so much for this great work!
Thank you. I am new to ImageJ, didn't know how to extract each tiff image from a tiff video. Thank you.
Hi, thanks for this great introduction. How do I create a macro, that works through a folder of files?
If you go to the menus: Process -> Batch -> Macro, you can paste in any macro and apply to an entire folder. There are some subtleties. See ua-cam.com/video/fU104OU3Kk4/v-deo.html and ua-cam.com/video/3qA-liZZKgc/v-deo.html for an example. Message back if you have questions
what do you mean by adding something reasonable 50? why 50
I think I meant to say something reasonable for the size of the image. The scale bar should be a easily extrapolated size. Too small and it's hard to extrapolate to the size of the image, and too large and it might as well be an axis. The brain does better with a bar that's about a 1/3 of the width (the largest I'd ever recommend), to 1/4, or 1/8 ish. All that and it makes sense to have round numbers that can also be extrapolated, e.g. 5, 10, 20 µm.
I think it's helpful to point out that prior to setting the scale size, we already know from the metadata what the microns/pixel ratio is (0.41um/px) assuming the camera was calibrated properly. Setting the scale bar to 50 isn't arbitrarily setting the scale of the features or morphometric tools. The scale bar tool is simply a visual to represent a size we know to be true based on the objective lens the image was captured through. Note that when the size is changed from 44 to 50, the line expands accordingly. Setting it to 100 would produce a scale bar twice that size.
@@heyjonbray Absolutely; thanks for specifically stating that. I may have glossed over the key point that Jon highlights regarding metadata.
Hi actually I want to do FEA of 3D model generated by imageJ. So in which format the data be saved. Is there any option to save data in .stl or .iges format.
3D model generation will be, most likely, volumetric rendering or generating meshes from given structures, isosurfaces etc. I'm not familiar with a way to output 3D files of that type from ImageJ/Fiji (post back if you find anything). I'd look at ParaView for a great open source 3D package.
Hi, I work with MSC. I have to make a merge of 3 fluorescence microscopy images. After the merge and adjust the colors I want to save the composite in .tif and .jpeg format and also the split in .jpge. Do you know a macro that allows you to do it? I don't understand informatics and it takes me a long time to click all the time. Regards!
I could certainly run through a macro that does what you need. Please make example files available and I'll put that in place.
How did you get the .oif file extensions? I am confused about that step
The .oif files are raw files created by one of our Olympus FV microscopes. Typically you'd want to save in .oib format, but the .oif is an options, and it saves all the data into an associated folder with the same title. The .oif file is essentially a header that points to the folder and it's contents.
hi thx for the tutorial, what about batch processing of this kind of image processing?
I'll certainly go over batch some more. Did you have any more specifics in mind? I'll cover something like A. VazS mentions.
Hi! Thank you very much for the video! Really good to know there is a way of batch processing!! I'm trying with my files and run into a problem. I have to adjust Window&Level for all my images with the same level between images (each channel have different numbers). However macro is not recording the changes of W&L. May I ask if there is a way to add it? Thank you in advance!
Window & Level is essentially a different way to set the min and max values. If you click on Set in the dialog it will propagate to the Record window.
Hey, can you please explain how the images relate to each other and give information in three dimensions?
The view to the RHS shows all of the column data that's 'under' the vertical yellow line, and the lower image, all the rows 'under' the horizontal yellow line. See ua-cam.com/video/U0SJyCLfqXs/v-deo.html for a 3D view of the same thing.
Hi, Can you create a movie from Ortho slicer? Thanks
Yes, please see the Animation tutorials. You can set the position of the ortho slice and Modify, and then set another position at a different keyframe. I typically set the view to be Orthogonal (Camera type on the right) and then hit Reset (bottom right), or use Image Processing -> Camera Functions -> Set The Angle Of The Camera (to mess around and somehow find the view I need in that strange coord system), and then use that view to scan the ortho slicer into and out of the page (don't forget to uncheck the volume in the scene, and you can select the slice in the scene to control the position too). I'll make a quick video of it soon.
Where I can get these data?
How do you add more options for the output file, for example to be able the MPEG-4 Movie option?
Under Properties, in the Advanced section at the bottom, then find Snapshot section and expand. Change the EnableAdditionalMovieOutputFormats to true and you'll see all the great options from older Imaris versions
any email to help contact you directly ?
Hi Reuben. Yes, use nantho2@emory.edu
These cells are mycoplasma positive...
Can you please tell why metadata is being used and not a regular image type also What is C matching?
Certain file types hold multiple channels and zsections, and using the header metadata allows you to start from the raw files and simply pull in the channel or z you're interested in. The c in this case is the channel number which runs from 0 to N-1, so 0,1,2 for a three channel image.
how can i split the overly , i alaways get the gray color when i do channel splitting
Instead of channel splitting, maybe use the the channels tool (Ctrl Shift Z) and then use the check boxes in composite mode to select the channels to display. If you do split the channels, then you can always change the colors using the LUT button.
Great work. From this video I learned the role of distance transform. Previously I am curious about the purpose of distance transform, Now I know that it could be used to estimate the nearset distance to an object, and also could be used to draw the skeleton of an object.