How to measure Fiber Diameter using ImageJ
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- เผยแพร่เมื่อ 11 ก.ค. 2023
- This ImageJ tutorial uses the GIFT.ijm macro to analyze the fiber diameter. This tutorial is for education purpose only.
www.ncbi.nlm.nih.gov/pmc/arti...
github.com/IBMTRostock/GIFT/b...
bigwww.epfl.ch/demo/orientation/
github.com/ijpb/MorphoLibJ/re...
github.com/IBMTRostock/GIFT/b...
![FIJI (ImageJ): Fiber Orientation and Direction [Directionality & OrientationJ]](http://i.ytimg.com/vi/tN0bEVsumJc/mqdefault.jpg)
Hi, thank you for the video! I've been struggling with ImageJ and your video saved me.
However, I'm not sure how to set the parameters for GIFT. Should I use the default ones?
I have more than 80 SEM images to process so I'm hoping to figure this out to not lose my eyesight having to mesaure all the fibers one by one lol I'd appreciate any help!
Hello, @user-wx8tw4iq1h thanks for reaching out. I believe it is better to change the parameters based on your image's intensity/contrast, orientation, and dimensions. These parameters would be used to determine the threshold, degree of rotation, and line length differences in each image. in addition you could use a batch process method to process many images at once.
here is how the GIFT functions:
The user input settings are applied to either a single image or a group of images in a single folder. Next, edge detection and thresholding are conducted, followed by the generation of a set of rotated copies. An opening line filter is used to extract horizontal edge segments in each rotational image, and the vertical distances between them are measured. Vertical distances are shown as a histogram, and a Gaussian fit is employed to determine the average fiber diameter.
Thank you for the wonderful video. I'm trying to use this program, but I'm asking because I'm confused about applying the pixel and the actual length.
I would like to set the scale bar to the length of the object measuring the length through the and set the scale bar length, but I would like to know if I should set it to 0.06 if it is 6cm.
ㄴIt might sound weird because I'm using a translator.
After practice, i will measure the diameter of the fibers
You are welcome. need to set the values in pixels. For example if 6 cm corresponds to 100 pixels then you need to input 100. All the best.
Thank you very much for such an excellent video. I'm very sorry my question might sound stupid, but is it possible to use the default parameter for fiber diameter analysis of any SEM image? What's the unit for the frequency of the fibers? Is it in µm, mm, cm, or arbitrary units? I'm a bit confused about how I should select the correct parameters for my image.
Hello Thanks for the question. I am glad you asked. The frequency unit will be determined by how the data is analyzed and presented in a specific study or research environment. For instance the frequency units can be "counts" or "percentage %". The unit of diameter here by default is "pixels". In the "new analysis" window users can manually set the scale into any unit of choice such as nm, um etc. This macro "GIFT" has been developed to measure the fiber diameter analysis of SEM images. Here is the link to the original publication "www.ncbi.nlm.nih.gov/pmc/articles/PMC9529089/" . Let me know if you have additional questions.
@@nrttaye4033 Thank you very much for your detailed explanation!!! I really appreciate it. Keep up the magnificent work.
@@bigdraco5008 That sounds great to me. Thank you very much. I have more upcoming videos lined up. Please stay tuned for more interesting videos like this by subscribing the channel.
How to iterate this over all ROI.e.g.cells
I will get back to you once I figure this out. Please stay tuned. Thanks
Hi! Thanks for sharing this valuable information. I just wondering if there is any efficient way to measure fiber length in the case of small nanofibers? Because I need to analyze a bunch of images >< Thanks for your kind reply
Hello, welcome. You might want to explore other plugins to measure the fiber length. could you please check if the plugin in this video would work for you th-cam.com/video/CP2A-Jt279c/w-d-xo.html.
Hi I am facing problem in installing plugin MorpholibJ and orientationJ into plugin folder, can anyone help?
Hello, are you using mac or windows OS? In addition, have you tried using the lastest version of the ImageJ and then install the plugins? Let me know if that worked.
Hi
When I tried to do batch processing of a single image in a folder. It is throwing me an error, FILE saving error(IOException):
"C:...(path) )The system cannot find pat). Can you please help me to understand why I am getting this error? It is saving Edges and filtered images till 135 degree and then throwing this error. Even I changed input and output directory and added 2 images. Still not able to overcome this.
Thank you
Hello, I am not quite sure why the error is. I tried with both single and multiple images in a folder for batch processing and I could find the output graph of all the images. Sometimes re-installing the plugins and macros again helps. Let me know if it still shows the error after that. May be you could reach out to me directly with some of your sample images for troubleshooting.
@@nrttaye4033 Thank you for reply. The main problem is the way macro reads the path. If I copy paste the folder path it takes "\" and it writes all the output files and graph. If I use browse option and locate the folder then it takes"\" and throws this error. I am working in WIndows computer not mac. How can I contact you over email? I have couple of recommendations regarding the tool. I can share with you if you are interested to include them in macro.
1. The user should have option to include maximum and minimum pixel length that should use to filter the distances calculated for each rotated image. This will avoid the macro not to consider all the readings.
2. Macro can calculate the average diameter or dia distribution for all the images together not for each single image. The user can do that separately. But if macro does the dia hist and gaussian fit for all the images that will be a great addition.
Hi
I am struggling to make this work. I am getting following error
"unrecognized command Morphological Filters in line 357 (called from line 213) run ("Morphological Filters, operation=Erosion=[Horizontal Line]radius=" + lineLength;
Can you please help me? I am not sure whether it is version problem. I don't have Origin Pro is it because of that?
hello, to run morphological filters the image rotation and thresholding needs to be maintained. according to the image type could you change the thresholding value? Let me know if that worked.
@@nrttaye4033 Thank you for your reply. I am not sure what has caused the issue. I reinstalled ImageJ and all the plugins in another folder. Fortunately it solved my issue. I do have a question. Why GIFT macro is not writing any data if I am analysing single image.
Same problem....😢
Hello, could you solve the issue?