Tutorial 03 - Image processing in imageJ, ZEN, and APEER

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It is important to understand the basics of image processing before learning to perform these tasks via python coding. This tutorial uses a simple image processing function as an example to demonstrate it in three different image analysis platforms, imageJ, ZEN Lite and APEER, respectively.
References:
Free ZEN Lite can be downloaded from: www.zeiss.com/...
You can open a free APEER account here: www.apeer.com
PS: APEER is an online image analysis platform that is free for academia, non-profit and individual use.

Опубликовано:

15 сен 2024

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Комментарии : 13

@mmshafique8491 3 года назад

INFORMATIVE.. thanks alot

@JwanKAlwan 3 года назад

thanks a lot for this great explanation

@almasgari 3 года назад

Hi sir, I create an account but does not show the same workflow you are displaying ?? I even could not download the Zen lite ?? can you help please ?

@direboy 3 месяца назад

can you make video about installation of free version of Zen lite? I just can't install it because it asks for license

@subhashiskar4403 Год назад

A great video sir. Just want a favour from you that is if you can make a video exclusively on zeiss zen software download and installation as it seemed to a bit complex to me. May be some of them who are present here also want it as it a vast software and people from many disciplines want to get access to it for their specific need.

@JwanKAlwan 3 года назад

I have one question please. all of this tutorials applied for microscopic images what if i am interesting in processing Ct-scan images are the techniques and explanation are the same for the CT-. Thanks

@ZEISS_arivis 3 года назад

Same techniques apply for CT scan images. Please watch all the videos as I cover both 2D and 3D (2D image stacks). But in general you can treat 3D data as stack of 2D images and apply most functions to one slice at a time.

@marioalbertoc.g.7466 2 года назад

Can I remove noise from my images with ZEN lite? For example, the precipitation of a fluorochrome?

@ZEISS_arivis 2 года назад

Zen lite has some basic functionality and I am not sure if denoising is included in the free version. If the noise is unstructured (random) you can try Noise2Void approach. You can use it in APEER.

@hassanedds3785 3 года назад

thank you for this such a great way of explanation, I have just one question, what do you think about Matlab comparing to Phyton in image processing?

@ZEISS_arivis 3 года назад

MATLAB is not free so many people outside of Universities may not have access to it. Python is ubiquitous now a days and many people are contributing towards developing useful libraries, especially for machine learning.

@bakethere8993 2 года назад

Hello, How do I convert many .tiff images to .czi images?

@ZEISS_arivis 2 года назад

You cannot write .czi files, yet. Zeiss may publish a library soon to allow for czi writing. As of now you can convert from czi to tif. If you want to write czi files, look into downloading the free version of ZEN (called ZEN Lite).