Hi Johanna, I hope you are well :) Do you know of any alternative to using Threshold in macro, so that it automatically matches the result of each image? Because each image generates different values, and there is no way I can provide a fixed value that works for the entire set of images (there are many)
@AnduneYavetil6 күн бұрын
You should publish this in Jove so I can cite you!
@johanna.m.dela-cruz6 күн бұрын
@AnduneYavetil, thanks for your support. This isn't something new...just wanted to make it easier for ImageJ/Fiji users to check out tools to do image analysis.
@ibowman_UCLA_BRAIN7 күн бұрын
This video is EXTREMELY helpful and informative. It is a challenge to navigate through all of the myriad algorithms available within FIJI, specifically regarding registration. Thank you.
@johanna.m.dela-cruz7 күн бұрын
@@ibowman_UCLA_BRAIN Thanks for letting me help you.
@selvamarin-k4o8 күн бұрын
hello,After stitching the pictures, there is a black line between each pair of pictures. How can I remove this boundary line?
@johanna.m.dela-cruz8 күн бұрын
@@selvamarin-k4o hello. When you acquired your images, did you have an overlap percentage for stitching?
@selvamarin-k4o8 күн бұрын
@@johanna.m.dela-cruz To be honest, I don't know the exact overlap percentage of my pictures, but when I tried to set an overlap percentage and compute overlap , my pictures could not be sewn successfully, When I don't calculate the overlap rate, the pictures could be stitched together normally
@selvamarin-k4o8 күн бұрын
@@johanna.m.dela-cruz I think the black lines between the pictures are caused by the uneven lighting of my pictures, but I don't know how to deal with this problem
@johanna.m.dela-cruz8 күн бұрын
@@selvamarin-k4o you could try applying a FFT bandpass filter. I have a tutorial on this in one of my videos: kzbin.info/www/bejne/iZvaq3aLjq55gJo
@selvamarin-k4o8 күн бұрын
@@johanna.m.dela-cruz thank you!
@rajaaalwodai574510 күн бұрын
Great video I followed all the step but for some reason it’s not loading when I press measure. Can you please help. Thanks
@johanna.m.dela-cruz5 күн бұрын
Hi there. I’m nit sure what you mean by not loading….do you have objects in the 3D Manager?
@dawidkrzykawski91612 күн бұрын
Awesome! Thanks for your hard work!
@rajaaalwodai574513 күн бұрын
Thank you for this video. I tried using this video as a guide to automatically measure the volume of breast lymph nodes in a T2 fat saturation MRI scan, which I took my self. I’m encountering problems and challenges with the threshold as it’s also highlighting / segmenting neighbouring structures with similar contrast. Also, I’m unsure of the min and max values in 3D object counter, as the values I’m putting aren’t allowing me to isolate the nodes alone. I’d appreciate your help as this image analysis is part of my masters research project. Thanks
@johanna.m.dela-cruz13 күн бұрын
@@rajaaalwodai5745 hi! Thresholding works best when there is a good contrast between your object and the background. Perhaps your image needs a different method of segmentation. Have you tried weka segmentation or maybe Labkit?
@rajaaalwodai574513 күн бұрын
@ Hi, Thanks for replaying. How do I do that? I’m trying to automate the segmentation and then measure the volume of the lymph nodes rather than manually segmenting each node. I’m doing this on an mri scan / a stack of images rather than an individual one. Can you please provide some assistance. Thanks again
@johanna.m.dela-cruz13 күн бұрын
@@rajaaalwodai5745 I do have tutorials on Weka Segmentation and LabKit. Try checking them out.
@rajaaalwodai574512 күн бұрын
@@johanna.m.dela-cruz Ok that’s Just to clarify, do these segmentation processes work on a stack of images ?
@johanna.m.dela-cruz12 күн бұрын
@@rajaaalwodai5745 yes, they do.
@claireseelingbranscomb278114 күн бұрын
Is there any way to set a ROI so that cells outside of it will not be counted? Additionally is there a way to keep the number labels on the 3D viewer? Or add them after the 3D image is generated? I wanted to look at multiple channels in 3D, but when I add an image, I keep accidentally selecting it and it keeps moving, is there a way to keep it stationary?
@johanna.m.dela-cruz13 күн бұрын
@@claireseelingbranscomb2781 hi there. Do you have 2 channels and would like to count objects in one channel using ROIs from the other channel? If yes, then I would give your first question a thumbs up. The 3D viewer is just one way to view your image in 3D. You would first have to merge the channels in your images before you do 3D reconstruction.
@claireseelingbranscomb27818 күн бұрын
@@johanna.m.dela-cruz Thank you for the reply. My biggest concern now is numbering the cells. Is there any way to add numbers to the 3D viewer?
@johanna.m.dela-cruz8 күн бұрын
@claireseelingbranscomb2781 I don't think the 3D viewer will show the numbers. You can try 3D Project or 3D Script.
@prathyusharns919215 күн бұрын
How to do caliberation for nuclear morphometry
@johanna.m.dela-cruz14 күн бұрын
@prathyusharns9192. You should be able to acquire morphometric measurements if you know the scaling for your images, otherwise all measurements you get will be in pixels.
@ZiwenHe-w5s15 күн бұрын
Thank you, this is helpful!
@ZiwenHe-w5s15 күн бұрын
Do you know how to extract the average thickness with standard deviation? Much appreciate!
@johanna.m.dela-cruz14 күн бұрын
@@ZiwenHe-w5s If you export your measurements into excel, you should be able to compute for the mean and standard deviation.
@claireseelingbranscomb278115 күн бұрын
I have two questions: 1. With the 3D Object counter, I can't get the numbers for the cells to actually show up. There are colored dots on the cells and table says there are cells but they have no numbering on the image. How can I get the numbers (I have already tried changing the size and checking & unchecking the option white numbers)? 2. Is there a way to merge the 3D viewer from from the 3D manager labels cells? I need to be able to see where the cells are related to the other channel of Nissl but when I tried to merge the channels I got an error that the files weren't the same type/size.
@johanna.m.dela-cruz15 күн бұрын
Hi @claireseelingbranscomb2781. Go to 3D OC Options first. Check the Maps' parameters and make sure Show numbers and White numbers are checked. To merge images, you have to convert one of them to match the other. For example, if the 3D Objects Map is 16-bit, check that your original image has the same bit-depth. othrwise, go to Image-Type and choose 16-bit.
@An_el_go18 күн бұрын
Hello Johanna, can i have your email address? I've some questions about stitching images Nice video by the way
@Asianbabyblue1719 күн бұрын
Hi am I able to get the macro for this?
@johanna.m.dela-cruz19 күн бұрын
@@Asianbabyblue17 Send me an email so I can send it to you.
@MrUnis20 күн бұрын
if (canSigma) run("Sigma Filter Plus", "radius=" + sRadius + " use=2.0 minimum=0.2 outlier stack"..................why for thresholding in 3D, it does not recognize this command.
@johanna.m.dela-cruz20 күн бұрын
@@MrUnis Macros are not my strong suit, unfortunately. Did you use the macro recorder while using the plugin?
@MrUnis20 күн бұрын
Hi, i am trying to do mitoanalysis but i am getting an error, unrecognized command Sigma filter plus in line 194...Could you help me here please?
@johanna.m.dela-cruz20 күн бұрын
@@MrUnis hi ! I think it has something to do with the way you installed the plugin. Are you using Windows or Mac?
@MrUnis20 күн бұрын
@@johanna.m.dela-cruz windows
@MrUnis20 күн бұрын
probably yes, because in 3D Treshold optimimize .....I did not get radius and outlier remover
@nickdenniston427120 күн бұрын
Hi! Thanks for a great tutorial. When I threshold the image using default settings, I see in the ROI manager that several (individual) mitochondria are getting counted as a single ROI leading to massive numbers in the analysis. Is there any advice on how to reduce this? I used the nyquist equation to set my scanning parameters and I do not see a difference.
@johanna.m.dela-cruz20 күн бұрын
@@nickdenniston4271 hello. Did you try the Optimize Threshold command first to determine the right settings for your image? Default settings work most of the time, but not everytime. You could also try deconvolving your images first before using the plugin.
@nickdenniston427120 күн бұрын
@ ive deconvolved the images and i have also tried a variety of threshold setting indicated by the optimize threshold command. The best setting i found is a block size of 1um and a C value of 16. With these settings i am not getting as much noise and it minimizes the issue of having multiple mito being grouped into a single ROI. I am now worried that this C value is too high and i am missing information. Any thoughts?
@johanna.m.dela-cruz20 күн бұрын
@ I would think that a high C value is actually ideal for a deconvolved image.
@fburton821 күн бұрын
Turi ip ip ip... very useful!
@BCBNarjis28 күн бұрын
My ImageJ crashes when I try to do the thresholding. I can't proceed further 🙁 I have tried uninstalling and re-installing ImageJ. Does anyone know what's the issue?
@johanna.m.dela-cruz28 күн бұрын
Hi @BCBNarjis. How big are your images? What type are they (2D, 3D, 4D)? Are you using Windows or do you have a Mac?
@BCBNarjis28 күн бұрын
@johanna.m.dela-cruz the 3D image is 108mb, and the 2D image is 4 mb. I tried both 3D and 2D threshold but they both crash the app without any prompt. I am on Windows.
@BCBNarjis17 күн бұрын
Hey. I had replied to the comment but somehow it didn't post and I didn't realise. Thanks for the quick response. I figured out that it was a memory issue. I allocated more memory and now it works fine. 😊
@BCBNarjis17 күн бұрын
I had a 3D image, 108mb in size and I'm on Windows
@putusixtinadewandari404328 күн бұрын
hi, i want to ask, how to make multiple circle analysis in one image?
@johanna.m.dela-cruz28 күн бұрын
Hi @putusixtinadewandari4043. Do you mean your image is made up of several circular objects? Have you tried thresholding?
@putusixtinadewandari404328 күн бұрын
@johanna.m.dela-cruz not yet, how to do it? can you explain, please🙏
@Dr_Shanin_Rouhi_1989Ай бұрын
good luck
@sheliangwang6105Ай бұрын
@johanna.m.dela-cruz, could you make a protocol to show a solution about this problem" Fluorescence signals at one emission wavelength were recorded with dual-excitation wavelengths (A and B), the a ratio of fluorescent intensity of A/B was obtained. Next step is to convert the gray scale of the ratio image into pseudocolors. "
@lokiiiii3333Ай бұрын
Hi there! Is there any way to reverse the segmentation? we have been given 5 images from SEM (ti, si, w, k, and ca), and we are looking to input these different rgb images in one final image. Can this be done on segmentation or will it use different approach? tnx
@johanna.m.dela-cruzАй бұрын
Hi @lokiiiii3333. Do you mean put your images together as a montage or merge all these images together? Segmentation is just a way to make object identification and analysis easier.
@lokiiiii3333Ай бұрын
@@johanna.m.dela-cruz thanks for the reply! what i meant was to merge 5 diff. images into one.
@johanna.m.dela-cruzАй бұрын
@ You should first convert your RGB images to 8-bit (Image - Type - 8 bit). Then, select Image - Color - Merge. The colors can be modified via LUTs.
@grudule8498Ай бұрын
Thanks a lot !!
@VaishnaviK-j5jАй бұрын
Thank you so much for the great videos! I was trying to create a 3D projection of the merge between the object counter and the duplicate of my original image, however I get a message saying that "The source images must have the same depth." May I ask how I can troubleshoot this?
@johanna.m.dela-cruzАй бұрын
@@VaishnaviK-j5j Thanks for watching. In order to merge 2 different stacks, they have to have the same bit depth. You can change one of them to match with the other stack. Go to Image - Type - to do this.
@VaishnaviK-j5jАй бұрын
@@johanna.m.dela-cruz Got it! It works now. Thanks so much:) Another question I had was related to why I'm unable to view the numbers on the 3D projection despite selecting "show numbers" on the maps parameters. Another strange thing is that when I view the results including volume, centroid volume etc I'm unable to see what serial numbers they correspond to. Sorry to bombard you with all these questions haha:')
@johanna.m.dela-cruzАй бұрын
@@VaishnaviK-j5j Did you check Statistics on the 'Results tables to show' in the OC Options? You can Redirect your results to your original image stack as well, just in case you are meauring intensities. As for the numbers, they are probably there...they're either too small or in a color that is similar to your object colors. Use a different LUT for your objects (e.g. glasbey on dark), The numbers are also in different slices of your z stack.
@simoneceron1915Ай бұрын
Hi my program freezes when opening the stl file Any suggestions?
@johanna.m.dela-cruzАй бұрын
Hi @simoneceron1915. Perhaps the experts in the image.sc forum might be able to help with this: forum.image.sc/.
@evanh1332Ай бұрын
Great video. It was very helpful for understanding the MorphoLibJ toolset and workflow. Are you aware of any way to provide quantification data?
@johanna.m.dela-cruzАй бұрын
Hello @evanh1132. Thanks for watching. MorphoLibJ also has analysis tools. You can check out some of these tools here: kzbin.info/www/bejne/j6mmkpaubpZqqsksi=Rh3OIxa8B4M-f8Pf
@sanyamjain4210Ай бұрын
Thank you for the video! My pixel width/height doesn't fall in the given range. It is way out 352 um :" what should I do for counting then?>
@johanna.m.dela-cruzАй бұрын
Hi @sanyamjain4210. Are your files large? If they are not really whole slide images, perhaps you can open your files in Fiji and use StarDist to segment the cells. Also, is the pixel size really that large? Perhaps there might be something wrong with the spatial calibration in your image.
@SoleneVacherАй бұрын
Thank you so much ! You made me understand 6 hours of class in 2 videos !
@johanna.m.dela-cruzАй бұрын
Glad this helped, @SoleneVacher. Thanks for watching.
@yanzheliu9092Ай бұрын
Many thanks!!!!!💯
@Patrick-bv7jpАй бұрын
very helpful tutorial!
@acooper6521Ай бұрын
This is awesome. Thank you for this video. Do you know if Diana allows for analysis of time-lapse images?
@johanna.m.dela-cruzАй бұрын
Hi @acooper6521. DiAna is more of a 3D image analysis tool (object-based co-localization and distance analysis). There might be a different plugin that caters better to what you want to measure in time lapse images.
@KathleenMoore-w6q2 ай бұрын
Dalton Ridge
@spanishflea6342 ай бұрын
I have let fluorescent agent (Protoporphyrin IX) diffuse into some gelatin samples with optical properties simulating that of human skin, and with SFDI I'm trying to estimate how deep the fluorescent agent diffuses. How should I model a PSF to de-blurr my images? I know the wavelengths and I assume a attenuation factor. Any ideas?
@johanna.m.dela-cruz2 ай бұрын
Hello @spanishflea634. I have no experience with SFDI, so I can't give you a definite answer to your questions. Is it considered an optical image? If it is not, then I don't think deconvolution has any scientific validation for these types of images. Perhaps what you need is an enhancement of your image (although I can't be sure about this since I don't really know what your image looks like). If you could share your image, maybe I can suggest some methods to enhance its quality.
@shruthib81762 ай бұрын
Hi, Thank you for the videos they are resourceful. I am trying to track cells in 3D to calculate their angular velocity. I would appreciate some help with this.
@johanna.m.dela-cruz2 ай бұрын
Hi @shruthib8176. I don't think TrackMate has analyzers that measure angular velocity. It does have features that track motility type and mean directional change.
@shruthib81762 ай бұрын
@@johanna.m.dela-cruz Thank you very much for getting back to me. I used the xy coordinates from the TrackMate to calculate the angular velocity.
@annisadwilestari44702 ай бұрын
Great content subscribed. Hallo, can you perhaps make video about how to count inflamation cell ilfitration on histology? Thank you so much, I really need it.
@johanna.m.dela-cruz2 ай бұрын
@@annisadwilestari4470 thanks for supporting my channel. I could try to do a tutorial like you suggested…I just need an image to work with.
@annisadwilestari44702 ай бұрын
Thank you so much for answering, it means a lot, because I'm currently struggle to learn how to do it. I'll be waiting for it.@@johanna.m.dela-cruz
@johanna.m.dela-cruz2 ай бұрын
@annisadwilestari4470 do you perhaps have an image i can use? You can email it to me if you’re ok with me using your image.
@annisadwilestari44702 ай бұрын
@@johanna.m.dela-cruz hey I'm actually have not a picture from my self. Is it okay if I took it from Journal/someone research and send you?
@johanna.m.dela-cruz2 ай бұрын
@@annisadwilestari4470 I guess i just need to know what exactly I’m working with or how the image would look like (since this is not a field I’m used to).
@oliviapietrobon52252 ай бұрын
Hello from Argentina! I've been following you for a long time, and your videos are always great! Do you have any on immunohistochemistry analysis? I know you sometimes organize courses, and I’d love to learn more about them. Thanks!
@johanna.m.dela-cruz2 ай бұрын
Thank you Olivia (@oliviapietrobon5225) for your continued support. What type of measurements do you want to do on your IHC images?
@oliviapietrobon52252 ай бұрын
@@johanna.m.dela-cruz Hello, I am analyzing images where I used immunohistochemistry to mark androgen receptors. Although it's not the same, when I saw your analysis in immunofluorescence, I noticed that the analysis is done for each ROI (Region of Interest) that you create. ¿Can I do the same in the case of immunohistochemistry? Another question, when you analyze each ROI, do you get a value for each one,To create the graph, ¿did you take an average of all those values? I hope my questions are clear. Thanks, Johanna!
@johanna.m.dela-cruz2 ай бұрын
@oliviapietrobon5225 As long as you arr able to segment the regions you want to measure, then, you can get measurements from each ROI. I am not sure what stain you used, but if you have DAB, quantifying intensity won’t be a sensible way to characterize antigen expression.
@oliviapietrobon52252 ай бұрын
@@johanna.m.dela-cruz Hello, I use de tunel technique and caspasa 3 (for this i use DAB), now another question, I see that you're making a graph of the measurements; I'd like to know if you're calculating an average of the values from each ROI. My concern is that sometimes the values can be very different between each ROI, wouldn't that result in a high deviation?
@johanna.m.dela-cruz2 ай бұрын
@@oliviapietrobon5225 yes, it's an avaerage.
@valdenilsonfelipe22462 ай бұрын
very good
@acufssdz123 ай бұрын
Stop using this disgusting music, you piece of shit. Just talk over it. Your tutorials would be better if you talked.
@Lam-m3l3 ай бұрын
Thanks for very good tutorial. Can you share the used dataset?
@johanna.m.dela-cruz3 ай бұрын
Hello @Lam-m3l. Thanks for watching my tutorial. Unfortunately, due to some permission issues, I can't share the images I used. However, there are several image datasets that you can use from this site: imagej.net/plugins/samples.
@Lam-m3l3 ай бұрын
@@johanna.m.dela-cruz Thanks for the info. I was interested in the convoluted-looking fiber-like first dataset that you used. Not necessarily microglia though.
@johanna.m.dela-cruz3 ай бұрын
@Lam-m3l You’re right…that was a z-stack of microglia.
@KritiAttri3 ай бұрын
Hi. Thanks for a great video tutorial. However, I am struggling to export data of multiple closed curves drawn in 1 image. Every time I save the data, it saves it only for Curve1. I want to save it for all the curves I draw in the image. Could you please help out? Thanks! :)
@johanna.m.dela-cruz3 ай бұрын
Hi @KritiAttri. On the right side of the Kappa console, you have to click on Curves and then select the curves you want to get their data exported.
@peterlkk3 ай бұрын
Thank you for your sharing. I have watched your 3D Image Deconvolution video. However, in that video, only one channel was applied for the deconvolution. In this video, two channels are involved. How should the deconvolution be done on multi-channeled 3D images? Could you give us some suggestions?
@johanna.m.dela-cruz3 ай бұрын
@@peterlkk Split the channels and run deconvolution (and psf) on both channels individually.
@jd96113 ай бұрын
Thanks for the great tutorials as always. I have a question, does curvature have a color mapping tool like local thickness?
@johanna.m.dela-cruz3 ай бұрын
Hi @jd9611. I don't believe Kappa has that feature.
@tritoniadiomedea3 ай бұрын
I can not tell if the source images were collected at arbitrary intervals, or if you used a stepper motor to get equal intervals. Are equal intervals necessary, or is the software able to just use the most focused pixels without knowledge of their z-position?
@johanna.m.dela-cruz3 ай бұрын
Hi @tritoniadiomedea. The stacks used in this video were acquired as transmitted light images in a confocal microscope, so step size was constant. However, if images were acquired at various intervals (manual focus adjustment), EDF would still be useful.
@kevinn15343 ай бұрын
I have a problem with my saving of plot data, it is not saving my csv z axis profile, only if I run the code several times I can see half or less of the overall data
@kevinn15343 ай бұрын
and adding "wait" steps doesn't work
@johanna.m.dela-cruz3 ай бұрын
@kevinn1534 Perhaps there’s something missing in your code.
@kevinn15343 ай бұрын
@@johanna.m.dela-cruz thanks for your reply... can I show it to you? I don't think is missing something, I literally use the macro recorder and I verify it.
@johanna.m.dela-cruz3 ай бұрын
@kevinn1534 you can email me. I’m not an expert in macros, but I can take a look at it.
@kevinn15343 ай бұрын
@johanna.m.dela-cruz thanks a lot 🙏 Can you share me your email pls
@sriti_hikari3 ай бұрын
Hi do you have any idea on how to measure the fiber orientation on a 3d-z-Stack?
@johanna.m.dela-cruz3 ай бұрын
@@sriti_hikari You can try Directionality or OrientationJ. My tutorial is here: kzbin.info/www/bejne/qn-Tk3iMqNqggMUsi=vxeAMMU906Wsts0z
@sriti_hikari3 ай бұрын
@@johanna.m.dela-cruz Hi thank you for your help- this will only give the orientation in the x-y-plane right? so the direction in z is not considered?
@johanna.m.dela-cruz3 ай бұрын
@@sriti_hikari Since each image in a z-stack is an optical section of your sample, fiber orientation shows the angle per slice. If you do a maximum projection of your z stack and then run the plugin, the orientation is based on the xy plane.
@richterdavidoliver77823 ай бұрын
Your Videos are excellent, I have done a bit of quantitative Image analysis, and I wish I had them back in the day. Many thanks for the effort you put into them.
@johanna.m.dela-cruz3 ай бұрын
It’s heartwarming to receive your positive feedback. Thanks for your support.
@usercvzu12563 ай бұрын
How can I make track mate for time lapse photos with cyanobacteria please? Thank you very much
@johanna.m.dela-cruz3 ай бұрын
@@usercvzu1256 You will first need to make sure you have a single file containing a sequence of your images. If you have several photos in a folder (File - Import - Image Sequence).
@MDIqbalHossain-d8v4 ай бұрын
hi..Thank you for the video. I was wondering if its possible to get only the 3D mask from these z stack. Like I just want the 3D mask from my 3D stack of images. Thank you
@johanna.m.dela-cruz4 ай бұрын
@@MDIqbalHossain-d8v hi! You can convert the label image stack into a binary stack by thresholding. Use a minimum threshold of 1.
@zahraahmadi22344 ай бұрын
hello. I have a question.would you please help me?I want to count the number of grafts inside the plates with the Fiji (filament detector). How can I do that .(can i have your email address ,I want to send photos)
@johanna.m.dela-cruz4 ай бұрын
Hi Zahra. If you go to my channel description, my email address should be there.
@zahraahmadi22344 ай бұрын
@@johanna.m.dela-cruz I can’t find there😅
@johanna.m.dela-cruz4 ай бұрын
@@zahraahmadi2234 If you are subscribed to my channel, under my name, you will find the statement "Listen, watch and learn..." click on more and you can view my email address. Sorry, I can't just advertise openly my email address. You would have to be on a laptop/computer (not phone) to see it.
@zahraahmadi22344 ай бұрын
@@johanna.m.dela-cruz I use phone and subscribe your awesome channel ( I don’t access a laptop or computer- would you please share your email address here)
@zahraahmadi22344 ай бұрын
@@johanna.m.dela-cruz I use phone and subscribe your awesome channel ( I don’t access a laptop or computer- would you please share your email address here)
@m359264 ай бұрын
What about if I want to make four quadrants of a circle in ROI and segment them to analyze 4 different area from the intersection of a circle and 2 lines (vert and horz)? Can I do that? I haven't seen anyone do this in ROI yet. Thanks
@johanna.m.dela-cruz4 ай бұрын
@m35926 I think you can do this with a grid. It might be a tad more complicated, but check out this video about counting objects in a grid. kzbin.info/www/bejne/nIG1dmukmrV5ncUsi=4EET_DzS8yNJbDoM