haesleinhuepf
haesleinhuepf
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Bio-image Analysis using Napari and Python
When using Bio-image Analysis using Python, Napari is one key application for interactive image data science. In this lecture we explore basics of interaction within Napari, e.g. to classify pixels and objects. We also take a guided tour through the Napari plugin ecosystem and take a deep dive in how to setup bio-image analysis workflows using the Napari-Assistant and how to export Python Jupyter Notebooks for reproducible workflows.
Slides: f1000research.com/slides/12-972
Exercises:
* haesleinhuepf.github.io/BioImageAnalysisNotebooks/20a_pixel_classification/interactive_pixel_classification/readme.html
* haesleinhuepf.github.io/BioImageAnalysisNotebooks/27_cell_classification/interactive_object_classification/readme.html
* haesleinhuepf.github.io/BioImageAnalysisNotebooks/70_workflows/napari-assistant.html
* haesleinhuepf.github.io/BioImageAnalysisNotebooks/70_workflows/notebook_export.html
Переглядів: 2 478

Відео

Generative Artificial Intelligence for Bio-image Analysis
Переглядів 1,4 тис.Рік тому
Generative Artificial Inteligence - and in particular large languge models - are changing the way we use computers. In this talk I explain the underlying principles and give examples how large language models such as OpenAI's chatGPT and technologies like LangChain can be used to do Bio-image Analysis. Slides: f1000research.com/slides/12-971 Exercises: haesleinhuepf.github.io/BioImageAnalysisNo...
I2K2020: Designing GPU-accelerated Image Data Flow Graphs for CLIJ2 and clEsperanto
Переглядів 7303 роки тому
... and deployment to ImaeJ, Fiji, Icy, Matlab, QuPath, Python, napari and C Workshow at the "From images to knowledge (I2K)" conference 2020 virtually at HHMI Janelia. www.janelia.org/you-janelia/conferences/from-images-to-knowledge-with-imagej-friends Part I 0:00:00 Introduction 0:06:04 GPU-accelerated image processing 0:12:10 Benchmarking.png 0:19:00 Optimal performance through smart memory ...
CLIJ: GPU-accelerated image processing for the life sciences
Переглядів 8603 роки тому
This talk gives a quick insight into CLIJ and how it delivers image processing techniques specifically for the life sciences, for studying cells and tissues in microscopy data. It was presented as a mini guest lecture demonstrating a use-case for the lecture series "Highly Parallel Programming of GPUs" by Dr. Guido Juckeland (HZDR Dresden) at the Faculty of Computer Science of the TU Dresden.
14c Applied Bio-Image Analysis Lecture 2020 - A Summary
Переглядів 1,3 тис.4 роки тому
A summary about what we learned in the 2020 lecture about Applied Bio-Image Analysis at BioTec TU Dresden 0:01:30 An Introduction to Applied Bio-Image Analysis 0:19:34 Filters don't do magic 0:30:10 Image Segmentation 0:38:19 Feature extraction 0:42:41 Tracking & Image Registration 0:44:42 Machine Learning 0:50:28 Bio-Statistics 1:04:46 Programming 1:11:28 Tools and Toolboxes 1:23:58 Open Sourc...
14b Image Registration in Fiji
Переглядів 2,2 тис.4 роки тому
Image registration in Fiji, introducing BigStitcher, Grid Collection Stitching, Pairwise stitching and StackReg The slides and materials are online available: git.mpi-cbg.de/rhaase/lecture_applied_bioimage_analysis_2020
14a Image Registration
Переглядів 13 тис.4 роки тому
Introduction to image registration, rigid, affine and non-rigid transforms
13b Multi-dimensional Image Processing in Fiji
Переглядів 6924 роки тому
Introduction to multidimensional image processing in Fiji with virtual stacks, projections and the Big Data Viewer. The slides and materials are online available: git.mpi-cbg.de/rhaase/lecture_applied_bioimage_analysis_2020
13a Multi-dimensional image processing
Переглядів 1 тис.4 роки тому
Introduction to multi-dimensional image data, challenges and basic theory behind potential solutions The slides and materials are online available: git.mpi-cbg.de/rhaase/lecture_applied_bioimage_analysis_2020
12d 3D Image Visualisation and Processing in Python using scikit-image, itk and napari
Переглядів 9 тис.4 роки тому
Introduction to 3D image processing and visualisation in Python using scikit-image, itk and napari The slides and example data are available online: git.mpi-cbg.de/rhaase/lecture_applied_bioimage_analysis_2020/tree/master/12_Volumetric_image_data
12c 3D Image Processing in Fiji
Переглядів 2,4 тис.4 роки тому
Introduction to 3D Image Processing in Fiji The slides and example data are available online: git.mpi-cbg.de/rhaase/lecture_applied_bioimage_analysis_2020/tree/master/12_Volumetric_image_data
12b 3D Image Visualisation in Fiji
Переглядів 1,2 тис.4 роки тому
An introduction to 3D Visualisation tools in Fiji The slides and example data are available online: git.mpi-cbg.de/rhaase/lecture_applied_bioimage_analysis_2020/tree/master/12_Volumetric_image_data
12a Volumetric Image Processing
Переглядів 1,6 тис.4 роки тому
An introduction to image processing in three dimensions and the Nyquist Shannon Theorem for choosing the right voxel size
11c Writing pythonic code [highres]
Переглядів 5994 роки тому
Best practices to organising python code and a quick introduction to object oriented programming The slides and corresponding Jupyter Notebooks are available online: git.mpi-cbg.de/rhaase/lecture_applied_bioimage_analysis_2020/tree/master/11_Hypothesis_testing
11b Hypothesis Testing in Python [highres]
Переглядів 4524 роки тому
An introduction to random numbers, inferential statistics and hypothesis testing in python The slides and corresponding Jupyter Notebooks are available online: git.mpi-cbg.de/rhaase/lecture_applied_bioimage_analysis_2020/tree/master/11_Hypothesis_testing
11a Hypothesis Testing [high res]
Переглядів 4704 роки тому
11a Hypothesis Testing [high res]
11c Writing pythonic code
Переглядів 3114 роки тому
11c Writing pythonic code
11b Hypothesis testing in python
Переглядів 2104 роки тому
11b Hypothesis testing in python
11a Hypothesis Testing
Переглядів 1284 роки тому
11a Hypothesis Testing
10c Bio-Image Analysis using scikit-image in Python
Переглядів 1,6 тис.4 роки тому
10c Bio-Image Analysis using scikit-image in Python
10d Processing tables with python using numpy and pandas
Переглядів 1,2 тис.4 роки тому
10d Processing tables with python using numpy and pandas
10b Python Programming: Conditions, data structures, for loops and functions
Переглядів 7994 роки тому
10b Python Programming: Conditions, data structures, for loops and functions
10a Method comparsion and Bland-Altman plots
Переглядів 18 тис.4 роки тому
10a Method comparsion and Bland-Altman plots
09b Scientific Data Analysis with Python
Переглядів 3,4 тис.4 роки тому
09b Scientific Data Analysis with Python
09a Descriptive [Bio-]statistics
Переглядів 1 тис.4 роки тому
09a Descriptive [Bio-]statistics
08a Machine Learning for Pixel and Object Classification
Переглядів 3 тис.4 роки тому
08a Machine Learning for Pixel and Object Classification
08c Machine Learning for Pixel and Object Classification in ilastik
Переглядів 3,8 тис.4 роки тому
08c Machine Learning for Pixel and Object Classification in ilastik
08b Machine Learning for Pixel Classification in Fiji
Переглядів 2,2 тис.4 роки тому
08b Machine Learning for Pixel Classification in Fiji
07b Trackmate
Переглядів 4,6 тис.4 роки тому
07b Trackmate
07a Spot detection and Tracking
Переглядів 2,1 тис.4 роки тому
07a Spot detection and Tracking

КОМЕНТАРІ

  • @poiremusclee9189
    @poiremusclee9189 Місяць тому

    you know a course is gonna be good when the lecturer got such a thick accent youtube sets the automatic translation to german

  • @Demonprinz1
    @Demonprinz1 2 місяці тому

    Massively underrated video. Incredibly helpful even for someone with not as much coding experience like me. Shot not though: napari.gui_qt() is depreciated and got replaced by napari.run() meanwhile.

  • @nummelo2141
    @nummelo2141 4 місяці тому

    cute cat

  • @sushantmarella2728
    @sushantmarella2728 5 місяців тому

    Hello, hopefully you'll see this. How would I loop through an ROI manager of straight lines and measure something on a profile plot for each of the lines? I'm having trouble looping through it.

  • @yadavghimirey
    @yadavghimirey 7 місяців тому

    Hi Robert, I wanted to sent a message to you in Twitter but looks like it is not enabled. How do I send you my queries which I can't do in comments? Thank you!

  • @rushik0104
    @rushik0104 10 місяців тому

    getting this error on vs code ValueError: _getfinalpathname: embedded null character in path

  • @mattd6908
    @mattd6908 Рік тому

    Thank you for the effort put into this. I especially appreciate the real-world examples and that you did show other software. Fantastic course!

  • @liliannabakinowska217
    @liliannabakinowska217 Рік тому

    That is so well explained! So helpful! Amazing lecture! Thank you so much!

  • @mariashilova4359
    @mariashilova4359 Рік тому

    Thank you very much, very clearly explained!

  • @bic1349
    @bic1349 Рік тому

    Thank you!!

  • @marinamalic7921
    @marinamalic7921 Рік тому

    Hi, thank you for this video! I have a problem because I want to analyze several images at once and would like to keep their original names in the output. Could you please help me with that?

  • @黄通-s4o
    @黄通-s4o Рік тому

    Do you have Chinese subtitles

  • @ndowidar
    @ndowidar Рік тому

    Man, I love this lecture! Thanks so much for putting it together.

  • @johnsonburgundypants
    @johnsonburgundypants Рік тому

    great job, thanks

  • @fadhilfp6
    @fadhilfp6 2 роки тому

    Can we use this plot to check changes happened to 2 groups of patients subjected to 2 different medications treatment through measures their values twicely (before and after) by the same technique and in comparing between them we found difference between them then we do this plot to check performance or it is not true since we use same apparatus twicely ?

  • @mehrinaz3466
    @mehrinaz3466 2 роки тому

    Great explanation! Thanks!

    • @mehrinaz3466
      @mehrinaz3466 2 роки тому

      Also I hope you apologised to your cat afterwards

  • @rubalsingh7885
    @rubalsingh7885 2 роки тому

    Hi Thanks to this video tutorial. Can we do this Segmentation in 3D cultured cells and if yes please make one video on 3D cultured cells Segmentation.

  • @aminsinichi
    @aminsinichi 2 роки тому

    Very well done!

  • @vikramkumar1955
    @vikramkumar1955 2 роки тому

    Hi Robert, Thanks for sharing these amazing videos. Do you have any textbook recommendation that maybe goes a little bit into detail about the underlying algorithms?

  • @darlinbebey3903
    @darlinbebey3903 2 роки тому

    Thanks a lot, it makes me can develop macros!

  • @Bai_Su_Zhen
    @Bai_Su_Zhen 2 роки тому

    I have a bunch of folders named 001-100 and inside of them I have series of pictures which I import into ImageJ. How do I make a cycle where it goes like open=path/*number of folder*/all the pictures, then does all the operations for the pictures from folder, then imports from next folder, does all the operations and so on? I only need to figure out how to introduce the variable into the filepath, the rest is done. So far I need to make 100 copies of the same command, manually rewriting the folder name in each of them which is annoying.

  • @seanhatton73
    @seanhatton73 2 роки тому

    Perfect pacing, excellent advice!

  • @DMAO208
    @DMAO208 2 роки тому

    very insightful lecture , much appreciated ! :)

  • @laraheuft6655
    @laraheuft6655 3 роки тому

    I used to be familiar with the bland altman plot.... a loooong time ago. Thank you for your lecture to refresh my foggy memory. Excellent work, i will follow you channel.

  • @boooringlearning
    @boooringlearning 3 роки тому

    great. subscribeable

  • @mengjulin1527
    @mengjulin1527 3 роки тому

    This video is superb! There's very few videos/tutorial teaching scripting in ImageJ, and this is probably the best one I've ever seen! Thank you so much! I am looking forward to digging more n more.

  • @melihcankilic5918
    @melihcankilic5918 3 роки тому

    Thank you so much for video from Turkey.

  • @KULDEEPSINGH-li6gv
    @KULDEEPSINGH-li6gv 3 роки тому

    subscribed

  • @Jacopolpo
    @Jacopolpo 3 роки тому

    Thank you so much, this course has been very helpful! Literally loved it

  • @thuli5209
    @thuli5209 3 роки тому

    This excellent! thank you very much!!!

  • @ricardodealmeida5485
    @ricardodealmeida5485 3 роки тому

    Excellent lecture. Thank you very much!

  • @martinfigares
    @martinfigares 3 роки тому

    Thank you so much for this video series! I struggle looking for content related to imageJ scripting, does someone know where can I find something related to imageJ javaScript scripting?

  • @yufengwang8115
    @yufengwang8115 3 роки тому

    Hi, thank you so much for posting this course! I am just wondering where I could find lecture 3b which seems to be missing in the playlist.

    • @haesleinhuepf
      @haesleinhuepf 3 роки тому

      Here you go: ua-cam.com/video/q4ISEWq6q4E/v-deo.html I also fixed the playlist. Thanks for reporting!

  • @saraharsalan8367
    @saraharsalan8367 3 роки тому

    Thank you so much! amazing lecture, as always

  • @saraharsalan8367
    @saraharsalan8367 3 роки тому

    Thank you so much! I am watching this lecture series starting from the first video and making notes on the slides I downloaded. I have learned a lot just from the first two lectures and I look forward to watching the rest

  • @nabarcheto7950
    @nabarcheto7950 3 роки тому

    Thank you so much!!!

  • @FA-cz3uh
    @FA-cz3uh 3 роки тому

    You are a german guy that why your lecture abnormal thank you very much

  • @Gabriel-cf3bw
    @Gabriel-cf3bw 3 роки тому

    You don't know how long takes for me to get here, thank you!

  • @akabuoguemmanuel2984
    @akabuoguemmanuel2984 3 роки тому

    This lecture series are what I have been looking for. Thanks alot

  • @niceday2015
    @niceday2015 3 роки тому

    thank you

  • @berylsk5049
    @berylsk5049 3 роки тому

    Hi dear! Thank you for this nice video. I would like to ask you about which software can I use for feature extraction? For example, can I use ecognition software?

  • @HelloHello-yf8dz
    @HelloHello-yf8dz 3 роки тому

    The voice is low, and not clear enough.

  • @NavidErde
    @NavidErde 3 роки тому

    I'm not at our university but you helped me out so much. Please continue your great work, much appreciated!

  • @3lpacheelpache58
    @3lpacheelpache58 4 роки тому

    Thank you Robert for your job, your time and your advices

  • @MRchalkie666
    @MRchalkie666 4 роки тому

    Thanks for the thanks @Robert!

    • @haesleinhuepf
      @haesleinhuepf 4 роки тому

      Thanks for your help and suggestions on the deconvolution part <3 :-)

  • @SallesGuerra
    @SallesGuerra 4 роки тому

    Amazing content! Thanks!

  • @tinashemukota1431
    @tinashemukota1431 4 роки тому

    Why does ImajeJ not give a summary of results of all the images processed in a batch? All the time I run a macro to count particles during batch analysis, i get results from just one image. How do I solve this?

    • @haesleinhuepf
      @haesleinhuepf 4 роки тому

      If you deactivate the "clear" checkbox in the particle analyzer, it will keep measurements from former runs in the table. Furthermore, reach out at image.sc if you have questions to the ImageJ community 😉

  • @waituntil
    @waituntil 4 роки тому

    Does anybody know how "Ilastik" is supposed to be pronounced?

  • @jazmyncoles-clarke5799
    @jazmyncoles-clarke5799 4 роки тому

    This was so helpful, thank you!

  • @k.m.taufiqurrahman9085
    @k.m.taufiqurrahman9085 4 роки тому

    I am facing problem to classify two different cells (one round and one circle). I need to keep round one in cell and circle one is no cell label. Always after trained both round and circle showed in cell types. How can I resolve this problem. I can send you the image if needed. Any help would be highly appreciated. Thanks for this videos, indeed it helped a lot.