Hi,

I would suggest you try out Icy (http://icy.bioimageanalysis.org) which we initially developed here at Institut Pasteur, but is free, fully open source and clearly community oriented.

It has a modern intuitive interface (Java, multi-platform), a synchronized viewer system, rich multi-ROI manipulation, 3D rendering via VTK (used in Imaris), has ImageJ built in to allow interoperability, and also provides a graphical environment to design entire image processing protocols (similar to LabView or Simulink, perhaps less complete but much more user-friendly).

The associated website has an integrated CMS that makes it particularly easy to submit plugins and protocols online and manage them (versioning, automatic bug reports etc). We use this platform everyday for our own, basic research, but also to deliver our tools to our collaborators (we specialize in 2D/3D spot & cell detection and tracking, colocalization, histology, live motorized microscopy).

Feel free to give it a try, and/or ask further question on the online forum!

Cheers

Alexandre

You can try to download Image J. It is free and does the job...

Good luck

I too prefer ImageJ. its easy to use and you can get more plug in depending on your needs.

ImageJ is great, but not super easy to work with for more complex problems such as classifying shapes based on their color. For such tasks I found the program ENVI (http://www.exelisvis.com/language/en-US/ProductsServices/ENVI.aspx) much more convenient to work with. It's not open source, but they offer a student license for about 100 dollars I think.

My experience is that image analysis is usually just the starting point of it. Once you have extracted the relevant morphological data from your images, you still have to analyze them, correlate them sith some other data, etc. It is very cumbersome to jump constantly from one software/enviroment to another for a single analysis.

I recommend Matlab: you can do everything with Matlab. As ar as image analysis goes, all the standard tools are in the "image processing" toolbox.

ImageJ is also available as FIJI, which may be easier to download and update (also free). There is a separate listserv devoted to ImageJ / FIJI questions outside ResearchGate that can be very helpful. It is considered best to have studied some tutorials before posting a question there, and also to attach the image in question. There are many plugins for segmentation; you might look first at k-means, color thresholding, and SIOX.

I worked with Image analysis from Olympus is excellent but it is not a free software. It can classify images according to their grey values, doing grouping, mosaic, calculate the shapes, sizes in excel sheets, enhance images and a lot of other jobs.

Hello

I have been usin ImageTool3 (http://compdent.uthscsa.edu/dig/itdesc.html) for a while, it was ok for size, shape, etc. determination and classification. Also inlcudes processing possibilities.

Good luck!

http://compdent.uthscsa.edu/dig/itdesc.html

Image J is easy to use. Also you can find in its web site a lot of variety plugins .

I prefer the ImageJ.

Image J is great, However, for microscopic quantification of individual cells (fluorescent density) or western blot analysis of specific bands, I recommend ImagePro Software!

I think you may find as many answers out there to this question as there are contributors to this post. Image J, FIJI and MatLab are open source and have many plugins, subscribers, and users because of that, but they aren't the easiest to learn for beginners. We are a teaching facility that works regularly with students new to the whole concept of imaging and analysis. We use Image Pro and Imaris here, both of which provide an easier interface and plenty of very useful , simplified and standardized tools. Online tutorials and YouTube training videos are part of their support, but they aren't cheap. Plugins for ImageJ, on the other hand, are written by multiple users and take some getting used to as they all work differently.

I believe your comfort level with Image Analysis and your budget will help guide your choices.

I should add that we do work on butterfly wing imaginig here occasionally, as we are affiliated with the Biology Department. Image Pro allows you to classify and sort by multiple classification categories (colour wavelength, size, morphologiy etc) with quick graphical tools. Filtering steps can eliminate noise in a variety of simple ways, and you can easily generate new images with the different classes organized in order or with overlays of your selection criteria with one mouse click. I recommend that you try a demonstration if you are new to image analysis.

Depends that you need to analyze you need compared advantages and disadvantages, because some of the programs need extra modules you must be considered that, I uses a Image Pro Plus.

Hi,

I would suggest you try out Icy (http://icy.bioimageanalysis.org) which we initially developed here at Institut Pasteur, but is free, fully open source and clearly community oriented.

It has a modern intuitive interface (Java, multi-platform), a synchronized viewer system, rich multi-ROI manipulation, 3D rendering via VTK (used in Imaris), has ImageJ built in to allow interoperability, and also provides a graphical environment to design entire image processing protocols (similar to LabView or Simulink, perhaps less complete but much more user-friendly).

The associated website has an integrated CMS that makes it particularly easy to submit plugins and protocols online and manage them (versioning, automatic bug reports etc). We use this platform everyday for our own, basic research, but also to deliver our tools to our collaborators (we specialize in 2D/3D spot & cell detection and tracking, colocalization, histology, live motorized microscopy).

Feel free to give it a try, and/or ask further question on the online forum!

Cheers

Alexandre

I think MATLAB software can be useful. If you know some basic programs for image analysis, the process will be smoothly.

ImageJ is great if you can find the right plugin. Sometimes, the plugins allow adjustment of variables, sometimes you just have to see if the defaults work. I would also encourage you to try Icy, as A. Dufour suggested above, they are relatively new and have an active development community that you can bounce ideas with.

In the end, what we've found is that consulting with a programmer allows you to tailor the algorithm to your exact needs do it does mean you pay for the service.

Yes, ImageJ works out, however fiji is a very good alternative:

http://fiji.sc/

I am using image analysis software by long time, I tried commecial or free programs, however my best choice at the moment is always Image J or the suite Fiji (which is ImageJ with a large set of plugins). There are many and many plugins for ImageJ and the real difficulty is to find to most convenient for you, sometimes this is the worst part of your duties. I must also say that I use regularly Image J for my practical undergraduate course of Image Analysis, and students are happy with this program (it's free so they can download at home and do practical work also outside the class) and find easily all the different possibilities.

I mostly use Fiji, a version of ImageJ, as it is free and contains a lot of plugins as standard that I find useful. Also, as it's fully open source, it allows me to give away software that i develop using ImageJ/Fiji. I find Fiji very good and it does do most of what I want, and has a very helpful user community. However, i have almost 30 years of experience in image analysis (IA) and am a reasonable programmer as well as a biologist. If no one on your research team has experience in IA, try to find somebody who does to get you going. I have also used commercial packages such as ImagePro plus and Leica QWin. The commercial packages are probably a bit better at manouvering you through fairly straightforward analysis routines, but if things get a bit more difficult, there is no substitute to understanding what IA procedures do and which ones to apply to a certain problem. If you want to learn image analysis (which I would recommend you do, it's a valuable skill) there are good books and web sites available and some use ImageJ.

the fiji distribution of imageJ http://fiji.sc has the tools you need and the community support to help you use it.

McMaster Biophotonics Facility has their own ImageJ package that includes many plugins. Their website also has detailed instructions re: each of these plugins (a big plus!).

http://www.macbiophotonics.ca/downloads.htm

Macbiophotonics imageJ plugins collection was a really good thing. But watch out. It's not been updated since 2009 according to the website. So of the plugins there are out of date and contain buggy plugins that have been fixed or totally re written in Fiji distro of imagej. Eg coloc2.

To Rob van 't Hof

What image analysis books would you recommend for graduate student level in a research lab?

Thank you

@Mahasin: seminal books such as "Digital Image Processing" by Gonzalez and Woods are good starting point (that one is regularly updated, the latest is the 3rd edition from 2008).

Then, all depends of your speciality, e.g. in the case of microscopy imaging, I would recommend "Microscope Image Processing" (http://books.google.fr/books/about/Microscope_Image_Processing.html?id=uGWmR0f_350C&redir_esc=y), which also covers a great deal of the basics behind the image formation process.

Dear Wilfredo,

The program Fiji or Imagej are good programs for Image processing and are open access. You can download it from this webpage http://fiji.sc/

Josep

In addition to the ones recommended by Alexandre I would also recommend "The Image processing Handbook" by John C Russ. For people serious about using ImageJ/Fiji I really recommend Wilhelm Burger · Mark J. Burge "Digital Image Processing An algorithmic introduction using Java". It is relativekly easy to read and contains many useful examples using ImageJ.

Thanks Alexandre, appreciated

ImageJ of course

I use Image J and at times Gimp

Image J

ImageJ

SCIRun from the Scientific Computing and Imaging Institute from the University of Utah is a very high level software unit useful for visualization of data sets.

http://www.sci.utah.edu/software/scirun.html

Additionally, Seg3D helps perform segmentation analysis and has real time 2D transfer function capabilities for volume rendering

http://www.sci.utah.edu/software/seg3d.html

Their website has a host of other software suites. Enjoy...

Image J!!!

I also have a very good experiences with imageJ. This program is very user friendly, intuitive and has very simple structure based on small engine supplemented by a large (!!!) number of plugins. If you have some experience in programming in Java then imageJ will be sure very good solution!

yes ImageJ is very useful software can be applied for any kind of quantification, i personally used for TLC analysis and northern blot and its free on the web

"CellProfiler" is exactly what you need (http://www.cellprofiler.org)

Visilog is a very powerful tool, combined with statistic can solve all your problems.

imageJ is ubiquitous and the price is right!

ImageJ or Fiji.

I have exp. with imagej fiji and icy. Personaly, I find fiji is the easist of the three. I had to learn the macro language to make life easy with image analysis. It is not difficult to understand and with google i found nice routins to do the essencial jops like opening and saving large number of images. Icy with different GUI is essentialy imagej the site provid some help but not as much or as clear as for imagej and fiji. Most of the users are french and accordingly discussions.

Learning java is recommanded if you are planning to modify plug-ins or to develop your own. Have fun.

@Shabana: I would like to correct your statements if I may: 1) Icy includes ImageJ for compatibility but is not 'essentially ImageJ' (you can say this about Fiji though). Icy has many plug-ins of its own (~150) and benefits from our rich graphical user-interface and user-interaction (ImageJ plugins don't benefit from this); 2) I am surprised with the statement that the discussions are in French. All our forum and its discussions are in english since our users are all over the world. Perhaps you have visited the forum and tested the software in the early days? Much has evolved since then, and we now strive to publish protocols and youtube videos to answer people's questions.

@ Alexandre. I had to re-install Icy today to see what is new. You have right there is a sensible improvements in the interface, number of plugins and the form in English. But ,,, the there still few tutorials and the videos are made on old version of the program. "Icy image analysis" in google search yields 460 posts. "ImagJ image analysis" yields 43 800 posts. I will be glade, however, to attend at Pasteur one of the formations organized by the department. Thanks for your post hoping it will be useful for all.

ImageJ is very good easy and free software

Is there a software which can calculate the parameters simultaneously from a real-time video?in a way that it can show the amount of parameters in every second?

Hi,

I would suggest you try with FIJI. It's a very good free soft for quantitative image analysis.

cheers,

Josep

Hi,

Image J is a good analysis software.

Daniela

Article Improved cytochemical method for detecting Jordans' bodies i...

Is there a software which can calculate the parameters simultaneously from a real-time video?in a way that it can show the amount of parameters in every second

In my opinion, Image Pro software by Media Pro cybernetics (http://www.mediacy.com/index.aspx?page=IPP) is by far the most superior image analysis software that I have use for quantitative analysis. I use, in tandem FIJI, which "Fiji Is Just ImageJ...F.I.J.I) for image enhancements. However, for true quantitative measures across multiple images in concert with identical parameters, Image Pro is far more sensitive and quantitative than ImageJ/FIJI.

I agree with Onur Guven

Regards

Daniela

I do not agree with Joshua at all. I have used both ImagePro and Fiji. ImagePro may be a better choice for people with no background in image analysis, but lacks some of the flexibility of Fiji, is a black box (you don't know exactly how it calculates the values you get) and I have no idea how you can state that it is more sensitive and quantitative. Is your background in image analysis, combined with programming knowledge? I suspect not.

Hi. I used ImageJ software before. It can be downloaded free. Besides, it also edits the image before image analysis.

We use the image processing toolbox from Matlab for most of our custom image analysis needs. It's very flexible and has many built-in functions that are useful, but does require you to write the code up yourself. Matlab also has the file repository on their website and many other kind people have posted algorithms that accomplish various things you may find useful. ImageJ has a similar repository I believe.

I used Optimas and Image Pro (both Media Cybernetics) in the past. Today I use Fiji (Fiji is just ImageJ) because of its flexibility (huge community, many plugins) and transparency (you know, what the analysis and manipulation is doing).

If you are a beginner in image analysis it is a good tool to learn, although a commercial packages suggests a faster start to get data.

You get to Fiji here: http://fiji.sc/Fiji

Image j 1.45S is free and very simple to be used. But Olysia m3 is very powerful.

I use Avizo Fire for image processing and analysis.. Avizo fire is quite powerful with a scripting interface where you can write your own scripts, interoperable with Matlab, can be used for high end image processing needs. I use it for correction of non-uniform illumination in stone-based materials before segmentation. It also have advanced image segmentation techniques that can be combined for better results. Avizo Fire is a commercial software but you the company gives our full version of the software for a short period for trial purposes.

At present，most of the Pro./sofeware for the digital image analysis on crop field testing, are interal cycle or self-developed programs. Some programs were avaialbe commercally, you may use them for research, such as Envi，ERDAYS, PCI， ect..

You may also follow the address: http://www.phenofab.com/; http://www.phenodays.com/ Phenodays2013; and coming ’phenodays2014; http://www.lemnatec.com/; http://www.keygene.com/; ect.

We have developed a method to quantify staining intensity. The software named TissueQuant that we developed based on this method can be used for quantification of a stained substance. This software can also be used to calibrate and interactively measure areas and lengths of objects in an image.

The details can be found here: http://www.ncbi.nlm.nih.gov/pubmed/21924792

ImageJ is free and user friendly.

No doubt, ImageJ and Fiji (Fiji Is Just ImageJ) are the best open-source image analysis software. There are tutorials all around that will allow you to set up your own analysis macros. Easy and powerful!

Best wishes,

Carles.

Http://www.robertstech.com/software.htm that web provide a lot of preference for image analyzer

Image pro plus programme 

You actually need a complete software like Olysia M3. but it is not free. Image J is good but not professional software. However, you may freely download and try it.

You can try with FIJI (=IMAGEJ)

I would recommend you to have a look to VV which is suggested for both quantitative and qualitative analysis.

Link (it is free):

http://www.creatis.insa-lyon.fr/rio/vv

Imagej is very good

 ImageJ  -  an open-source image analysis software. It is easy and intuitive to use.

5 Free Image Analysis Software Tools for Microscopy -

http://www.stressmarq.com/Blog/Stress-Reducers/Top-5-Free-Image-Analysis-Software-Tools-for-Micro.aspx#sthash.VkN9JGCQ.dpuf

I use Image J and GIMP. They are good for few individual images. If you are thinking of getting data for QTL analysis you need precise data.

1. To do one by one, you may try: Resemble.js  [https://huddle.github.io/Resemble.js/  ]

Record the RGB+ brightness values one by one.

 2. To work on many images in high throughput scenario : CellProfiler Analyst is worth trying. http://www.biomedcentral.com/1471-2105/9/482

Hi All,

Firstly, thanks very much Wilfredo for posting such a helpful question. It turns out our previous reply recommending MIPAR has done wonders to spread awareness, and helped put MIPAR in the hands of many, who have used it to efficiently solve a wide range of problems -- that is out mission. Our user feedback has been so phenomenal, that we wanted updated this post to make sure users here get the most up-to-date information.

MIPAR has grown tremendously in its first year, and has continued show itself as perhaps the most flexible, yet straightforward image analysis package out there. Our 1-on-1 support is something many agree no other package can match, amplifies users' capabilities with MIPAR, and allows for a fantastic interdisciplinary exchange. Many of our users have implored us to work even harder to spread the word about MIPAR's capabilities, as they empathize with others who face the frustration and limitations of other other packages. So, that is what we are going to do.

I strongly encourage anyone who is unfamiliar with MIPAR to review its design and capabilities, and give it a free try at http://MIPAR.us. I admit my viewpoint is biased as its primary developer, so I invite you to review what others in community have said:

• I have used them all...ImageJ, commercial ones...there's just nothing like MIPAR. It's amazing.  Adam/Metallurgy
• I have to say it is more intuitive than other programs I have used, so that’s a big advantage!  Kim/Geology
• MIPAR's flexible recipe functions were able to overcome the limitations I experienced in other image programs.  Chris/Plant Science
• MIPAR is a great program. The idea of 'Recipes' is especially useful. I can recommend it for all researchers who need segmentation for their work.  Lazar/Nano-Particles
• It's so cool...a big kudos to you guys.  Raphael/Physics

I and my team are here for any questions or needs for assistance 24/7/265.

Cheers,

John

Go with ImageJ or its uplifted version FIJI. It is free, fairly easy to use and open-source. Anything else of the same caliber are expensive (e.g. MATLAB, IMARIS).

We have released a free toolbox for ImageJ that makes image calibration and measurement easy for quantitative analysis of reflectance images, or even cone-catch images for human/animal vision tasks. All that is required is a camera that can shoot in RAW and a grey standard.

Something that few people realise is that almost all images produced by cameras/scanners will be highly non-linear (they have to be to squeeze onto the dynamic range of a computer monitor), making quantitative colour or luminance measurements inaccurate unless the images are first calibrated.

Our toolbox uses 32-bits/channel image processing throughout, resulting in lossless and extremely precise linear image processing that preserves all the detail recorded by the camera (normally 12 or 14 bits/channel). The toolbox also supports combining multispectral images, allowing for visible and UV images to be combined for creating 'animal vision' images.

Below are links to our open access paper, and my website where you can download the tools.

http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12439/full

http://www.jolyon.co.uk/myresearch/image-analysis/image-analysis-tools/

Article Image Calibration and Analysis Toolbox – a free software sui...

We recently developed a free and open source (quantitative) image analysis solution named IQM (see http://iqm.sourceforge.net/ for a free download and http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0116329 for the corresponding publication). It offers a broad variety of preprocessing tools as well as measurement methods, furthermore ImageJ with all its availability is "integrated" as well.

If you need a customized solution for a specific task, please feel free to contact our (commercial) start-up in the field of quantitative biomedical image analysis - KML vision: http://www.kmlvision.com

I recommend Weka segmentation toolbox embedded in ImageJ. It is user-friendly, and powerful, RAM-consuming toolbox which uses statistical data mining algorithms to classify the texture. It is different than the conventional color thresholding as it calculates the statistical properties of adjacent pixels for any given pixel. Well, if you somewhat need the quantitative results over the whole image, any software that uses a color-thresholding method will already be useful. But, if you need quantitative results over discrete elements on an image, then Weka or any data mining algorithm will be necessary. 

Visit to explore the operation and applications of free, thoroughly documented CMEIAS Bioimage Informatics softwares designed to strengthen ecological research using digital image analysis. Our CMEIAS Color Segmentation and CMEIAS Image Analysis applications would be directly useful for your studies to classify butterflies using CMEIAS pattern recognition algorithms for size, shape, fractal geometry, and color. The website includes a comprehensive listing of linked publications using CMEIAS. Contact me if you want to collaborate.

اخى الحبيب دكتور سامح -- مليون الف سلام لك والاسرة الكريمة

بخصوص السؤال السابق

برنامج الكيوسار

يمكن ان يتنبا بافضل مركب كعلاج وبشكل نظري

وكذلك هناك اسلوب اخر وهو برنامج docking

حيث يدخل المركب الى داخل الكهف النشط بالانزيم ويري هل هيلبس فيه كويس -- ههه- ولا هيتنافر معاه ويستطيع ان يتصور كيف يتم الارتباط

ويسمي موليدرو او هايبر كيم

ويمكن ان نجلس سويا ونشوف

او نعمل محاضرة بالقسم وهكذا-- وفقكم الله

اخوك ابو اليسر

Hi!

You might give WIMASIS a try!  (https://www.wimasis.com)

WIMASIS platform offer a wide range of standard products which covers the main research lines in Life Sciences framework (Angiogenesis, Cell Death, Proliferation, Migration...)

However, since most research is unique and difficult to standardize, we could provide our technology to develop a custom solution that best fit your needs.

If you want to know if we can help you out, just initiate a free Feasibility Study in our myWim Platform (https://mywim.wimasis.com/)

https://imagej.net/Welcome

ImageJ

Digimizer,toupview

If you have a lot of images to analysis, I would recommend Cytoinformatics. LLC. It is very fast and will help you save a lot of time. Contact me at       [email protected]      if you are interested. 

Our CMEIAS Bioimage Informatics software is designed to analyze object shapes, sizes, classify microbial morphotypes, perform advanced color segmentation / classification. Free downloads of the software components are available at our project website and includes an extensive list of online-linked scientific publications at the Publications Using CMEIAS webpage. The next upgrade (version 4.0) is scheduled for release in winter 2019, and it will include over 100 new analytical features for image analysis of object sizes, shape, luminosity, and spatial features. Contact me if interested . Regards, ---Frank Dazzo.

I use ImageJ to "manipulate" images https://imagej.net/Welcome

IPP

I am pleased to announce our Deep Learning Beta Program. The solutions we've seen this tech pull off recently have been absolutely incredible. We are accepting applicants for our beta program if interested: https://forms.gle/3fGv9ZgfKLt9YhqF7

Clemex And Image J

ImageJ

https://imagej.nih.gov/ij/download.html

Micro-Manager

https://micro-manager.org/

CellProfiler

https://cellprofiler.org

Some do Acquisition & Analysis:

NIS-Elements

AxioVision

MetaMorph

Zen

Slidebook

Micro-Manager

Some do presentation:

Photoshop

Gimp

Some do Image Analysis:

Avizo

ImageJ

MATLAB

Imaris (3D visualization)

CellProfiler

Hello, I am also looking for recommendations for an automated digital image analysis software in order to compare the conditions of a wallpainting. I have a scan of a historical black and white photograph, made right after the execution of the wall painting over 100 years ago and an actual digital photograph. The wall painting has been altered due to damage by a fire, restoration measures like retouching and inpainting. Most of the changes are very obvious but some are more subtle. I would like to use a tool/software, which is automatically recognising changes in shapes and/or lines and is maybe even capable of mapping them. Any recommendations highly appreicated! Thank You!