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Harvard Center for Biological Imaging
США
Добавлен 12 фев 2016
A compilation of microscopy related lectures from the staff and guests of the Harvard Center for Biological Imaging.
Introduction to Cell Profiler
Beth Cimini gives an introduction to Cell Profiler, an open source environment for image analysis.
Просмотров: 60
Видео
Intro to FCS and Dynamics Profiler
Просмотров 81Месяц назад
Linda Liang gives a review of FCS and dives into next-gen FCS in the form of Zeiss' Dynamics Profiler (DP). DP has the added advantages of working with brighter cells and determining the direction of molecular movement.
Intro to live cell imaging
Просмотров 142Месяц назад
Heather Brown-Harding discusses the many aspects of live cell imaging including environmental considerations, hardware options, methods for fluorescent labeling and several specialized live-cell imaging techniques.
Intro to STED
Просмотров 116Месяц назад
Doug Richardson refreshes our knowledge of fluorescence and point scanning confocal before delving into the weeds of STED microscopy. If you ever wondered how it works, here's a quick overview.
Introduction to expansion microscopy
Просмотров 3,3 тыс.Год назад
Heather introduces us to the concepts and practicalities of performing expansion microscopy. This includes sample preparation, labelling and imaging.
Data storage and Image Analysis at the HCBI
Просмотров 335Год назад
Doug Richardson describes the new data storage and image analysis infrastructure at the HCBI. This includes over 2PB of storage and multiple remotely accessible workstations with lots of RAM, many processors and huge GPUs!
How to choose your microscope at the HCBI
Просмотров 2262 года назад
Kwasi gives an introduction to the many microscopes available at the HCBI and some tips on how to choose the right one for your research!
Using the AI Sample Finder on the LSM 900 confocal microscope
Просмотров 1,5 тыс.2 года назад
Chris introduces us to Zeiss' new AI sample finder and shows how it streamlines the set up of an experiment involving multiple samples on a slide or dish.
Introduction to 2-photon microscopy
Просмотров 3,5 тыс.2 года назад
Doug Richardson introduces the concept of 2-photon microscopy.
Introduction SIM2 acquisition and data processing
Просмотров 2142 года назад
Chris Hellriegel introduces the new SIM2 processing module. SIM2 can increase the resolution of a standard Structured Illumination microscope below 100 nm. Here, Chris introduces the theory behind SIM2 and demonstrates how to perform SIM2 image processing in ZEN.
Data storage and analysis infrastructure at the HCBI
Просмотров 2513 года назад
A brief history of past data handling and a description of the current (2021) storage and image analysis project at the HCBI.
Imaging and clearing organoids
Просмотров 2 тыс.4 года назад
An introduction to fluorescence microscopy methods for imaging and clearing organoids.
Using pre-trained ML algorithms for segmentation
Просмотров 1,7 тыс.4 года назад
An introduction to commonly available pre-trained machine learning algorithms for segmentation of light microscopy images.
Object and pixel-based colocalization
Просмотров 9 тыс.4 года назад
An introduction to the theory behind pixel and object colocalization methods
Colocalization analysis in ZEN
Просмотров 6 тыс.4 года назад
This video outlines all the features of the colocalization module in Zeiss' ZEN software. This was performed in ZEN Blue version 3.1
live cell imaging, photobleaching and phototoxicity
Просмотров 1,3 тыс.4 года назад
live cell imaging, photobleaching and phototoxicity
Manual object segmentation in Vision 4D
Просмотров 2414 года назад
Manual object segmentation in Vision 4D
Introduction to open source machine learning-based segmentation options
Просмотров 4454 года назад
Introduction to open source machine learning-based segmentation options
Introduction to the ZEN Blue Intellisis module.
Просмотров 2,7 тыс.4 года назад
Introduction to the ZEN Blue Intellisis module.
Introduction to automation in ImageJ and Fiji
Просмотров 13 тыс.4 года назад
Introduction to automation in ImageJ and Fiji
Image analysis pipelines with KNIME and Ilastik
Просмотров 8034 года назад
Image analysis pipelines with KNIME and Ilastik
Introduction to Lattice SIM and Single Molecule Localization Microscopy
Просмотров 6185 лет назад
Introduction to Lattice SIM and Single Molecule Localization Microscopy
makes me wonder if 2-ph can be used for killing tumor cells by increasing the pulse frequency to actually heat and denature the cells in the target location
Hello sir, i am using zen blue 3.9, but colocalization option is showing in the left pannel, so can you give me any suggestion, where can i get this option.
It may now be a module that requires an additional payment. Go to >Tools>Module Manager and see if Colocalization is available on your license. If it is, the tab to the left of the image window should appear when you open a file.
Awesome talk!
Oh hi son!🥰
Thank you!
Thank you.
nice pictures, but 0 info on detectors? sad
35:59 made me finally get it
Huge fan of the video! Noticed a small issue on the slide at 10:15 -- it should be λ^-4, not λ^4.
Can you tell me how to do ground truth annotation with black background and a white dot to represent object (mask)
Hi, Thanks for the explanation. what are these different series that open when I am trying to open one image? and how to choose the right series? originally, I was thinking that these series are the images of different samples I have taken on the microscope. if this is the case, then how can I know which image is which? because I have named every image differently for example control, treatment 1, treatment 2. and the series do not mention that.
@Harvard Center for Biological Imaging the macro is giving me an error that line 3 can not start with#@. when I remove this it gives anothe error '.' expected in line 3. i am not programming guy. But what does it mean? I am using imageJ.
help
Nice and concise presentation. Great job and well done. Very useful. Thanks
super interesting and well explained video, thanks for this!!
nice video ty
Thank you for this nice overview!
i cannot open sample image in FIJI. it shows blank
Do you have any demo videos with actual confocal images... Pls guide
It was an eye-opener for me. Thanks for uploading this educational video.
I enjoyed this and it was helpful learning about the processing pipeline, one thing I didn't see is how to calibrate and I believe this is important and I have not learned how to properly calibrate, do you have any idea how I could learn how to properly calibrate my images?
Great Tutorial! Is there a macro script available? This would be perfect!
Awesome, thanks!
I have an area and want to measure its value. So i put a polygonal figure to the place i want to measure it. I go to analyze than measure. Now instead of a picture, i want to analyze a video with 100 pictures. The place I measure stays the same. How do I do that without pressing measure after every picture?
Can we get spectral line analysis of EDS map data of 5 elements? Is it possible to have y axis in terms of atomic fraction?
17:45
Thank you very much for this training!
Great talk! thanks
Hey, thanks for your video. It was wonderful to learn so much about ImageJ. I just had a query, how to measure the velocity of a rising bubble in any solution using Image J?
Hello I have a query, how to calculate probably paramter for irregularities (PPi)
Thank you very much for the Tutorial! Do you have any advice for automated quantification for IHC-stained muscle fibers? I have to count the positive fibers(not cells) and have been doing it manually. Thank you in advance!
This was a very useful guide! Thank you for uploading it!
What is the software you use to piece things together if you are imaging the brain from both sides (i.e. rotate 180 degrees because of limited working distance)?
Thank you!!
thanks for sharing. It's a pity though video was taken from a far distance and some details are not visible
Super helpful. highly appreciate it.
I took pic with my camera and I have some refexion on one part of the zon I want to mesure. Because of the flash I can not anything. Is it possible to suppress it ?
I am afraid not, you either have to cut out your artifact (flash) or retake your picture.
@@XxXnonameAsDXxX Okey thank you for the answer !!
@@Archimede5917 No problem. Artifacts are very usual even with relatively good microscopes, you can have dust, uneven lightning etc that can cause you extra problems. You will get used to it
Apparently blobs.gif is an image of gold particles, not nuclei.
Thanks, that's the first video where the SIM tricks are explained. The audio is horrible, but there is the meat.
Hi! Thank you so much for all the help. I was wondering if the macro at the end is available somewhere? It would help me a lot with my bachelor end project on cell lineage tracing!
Hi. I am wondering if I could use this software to analyze normal pictures? They will come from a normal camera (JPG, Panasonic Lumix DC-FZ80)
legend! thank you
Thanks for that! COuld you please tell me how do I use the erase tool? Right now it is just blackening the area when I am using the erase tool. Not sure why is it so. thanks.
Where can I see the part before this one? Thanks
here - ruclips.net/video/BrNtHKDbTk0/видео.html
How do we use it for calculating porosity
Hi. Do you know if there is a way to manually cancel detected 'Blobs' during tracking analysis? or to manually scrub noisy areas so that they are not misidentified during binarization? Thanks
When you say 'memory' at the start you mean RAM (random access memory) right?
Yes, that's correct.
@@harvardcenterforbiological8767 thanks for replying even though it was a silly question. just wanted to make sure. I've been trying to use ImageJ to track insect locomotion but it keeps crashing when I try to import an mp4, do you know if there is a pluggin that I need to enable to allow it to function?
To export scatter plot data: Right click on the scatterplot -> Copy or Save data (can be imported directly into Graphing SW)
Thanks a lot for this useful tutorial! In terms of doing batch analysis of multiple images, can the scatter plots be exported? Not just as images, but for import into different software, for example: can scatter plots from different images be combined (for example to show anti-correlation in one set of images and correlation in the second set of images)?
you are amazing, thank you!