Science topic

Segmentation - Science topic

Explore the latest questions and answers in Segmentation, and find Segmentation experts.
Questions related to Segmentation
  • asked a question related to Segmentation
Question
7 answers
I have build a unet model for image segmentation when i train the model the dice score become greater than 1 . Is there any explanation of this problem?
Relevant answer
the dice coefficent in vgg16 with skip connection is better than u net
  • asked a question related to Segmentation
Question
5 answers
For an amino acid of size around 1000 aa, during the energy minimization step, I am not able to go beyond because it shows, "segmentation core dump", I have tried sudo get update and sudo clean all command to clear the cache memory, but nothing works.
Could someone please help me out with solving it via any other actions?
Relevant answer
Answer
Hetvi Shah after running this command " gmx grompp -f minim.mdp -c str_solv_ions.gro -p topol.top -o em.tpr"
run: gmx mdrun -v -deffnm em -nt 12
where -nt is the number of threads, maybe your laptop consists of 8 or more cores (the number of the logical processor is double to the number of cores) so you can assign it accordingly. you can check the number of cores on your laptop by typing on the search bar "system information" and you can easily find how many cores you have.
best of luck
  • asked a question related to Segmentation
Question
1 answer
As segmental allopolyploids originate from hybridization between closely related species with partially differentiated genomes whereas true allopolyploids involve hybridization between distantly related species.
Relevant answer
Answer
Ramanjot Kaur, I think you partially answered your own question correctly. The more closely related the two parental species are, the more similar the homeologous chromosomes would be. Therefore, the chance would be greater that homeologs would happen to pair with each other during meiosis or that multivalents would form instead of pairing only between the within-species homologs. In segmental allotetraploids, this is more likely to occur in some homeologous sets than others, perhaps due in part to chromosomal rearrangements.
I think it's helpful to see allopolyploidy as a range of chromosome pairing behaviors rather than something with discrete categories. Describing the actual chromosome pairing behavior in a polyploid is probably more important than what you call it.
  • asked a question related to Segmentation
Question
1 answer
Dear all
Anyone know the solution of the following error of boltztrap code? However this error may be occurs due to job memory issue.
================ BoltzTraP vs 1.2.5 =============
6
XXXXXXXX
1 0 0 1
0 1 0
0 0 1
1 0 0 2
0 -1 0
0 0 1
0.133932982687095 -0.757999481233344 5.000000000000000E-004 npoints
1784
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
BoltzTraP 000000000047B79D Unknown Unknown Unknown
libpthread-2.23.s 0000149521A37390 Unknown Unknown Unknown
BoltzTraP 00000000004588C0 Unknown Unknown Unknown
BoltzTraP 00000000004575C8 Unknown Unknown Unknown
BoltzTraP 000000000042C1E6 Unknown Unknown Unknown
BoltzTraP 00000000004111BD Unknown Unknown Unknown
BoltzTraP 000000000040342E Unknown Unknown Unknown
libc-2.23.so 0000149520FBA830 __libc_start_main Unknown Unknown
BoltzTraP 0000000000403329 Unknown Unknown Unknown
11.4u 0.0s 0:11.43 99.8% 0+0k 0+1256io 0pf+0w
Relevant answer
Answer
Play with the Number of allotted nodes and Memory. Possible reasons: too much memory requested; executable or mathematical libraries compiled for different hardware.
  • asked a question related to Segmentation
Question
4 answers
I am doing Finite Element Analysis of spirally reinforced concrete columns on ATENA 3D. I am perplexed while defining the spiral reinforcement as there is no option available for it. So far what I have understood is I need to define joints for spiral then connect them using line segments. For this option, I need to calculate the coordinates of joints manually, which is surely a hectic. If you can help me then please do.
Relevant answer
Answer
I would highly recommend importing AutoCAD geometry for spiral
It can be done quickly (maybe this answer could help future users)
  • asked a question related to Segmentation
Question
3 answers
I want to train a CNN to segment Ground Glass Opacities (GGO) in Lungs CT-scans.
I would need a dataset with CT scans and corresponding masks indicating for every voxel if it is GGO or not (i.e. the ground truth for the segmentation).
Do you know any dataset like that?
Many thanks for your help!!
Relevant answer
  • asked a question related to Segmentation
Question
3 answers
While I was researching for transfer learning, I saw that people are replacing encoders with VGG-16 weights and only training the decoder part of the network.
But in some representations (like this : (https://www.researchgate.net/profile/Song-Toan-Tran-3/publication/348025327/figure/fig10/AS:977249813684225@1610005920687/Visualization-of-a-feature-maps-from-each-layer-in-different-models-and-b-the.png)) shows that image segmentation also happening in encoder layers too. And based on my research the last layer of the encoder, segmentation is already done. We are just trying to rebuild that segmented image to high resolution.
But if we do transfer learning and freeze the encoder, we will not have that segmentation map (a very high-level feature) from the encoder part.
And now I am so confused. How is it possible to extract a perfect segmentation map by freezing high-level feature extractors? (Example code here: (https://www.kaggle.com/code/kmader/vgg16-u-net-on-carvana/notebook))
Relevant answer
Answer
While researching for transfer learning, I saw that people are replacing encoders with VGG-16 weights and only training the decoder part of the network. But some representations show that image segmentation also happens in encoder layers too. And based on my research the last layer of the encoder, segmentation is already done. We are just trying to rebuild that segmented image to high resolution.
  • asked a question related to Segmentation
Question
1 answer
Is having two different hypotheses on the same data amounts to multiple comparisons combining both hypotheses?
For example, I performed the connectivity analysis among 128 EEG electrodes to find out significant functional correlations among pairs of electrodes. Then used these significant connections to test the second hypothesis that in which frequency band these connections are different across eight emotion groups.
I understand here that hypothesis-1 is to infer (with FWER procedure) the significant connections among 128x128 comparisons and hypothesis-2 is to find out the frequency bands which show maximum distance among emotion groups in terms of functional connections. Following are the statistics about the data:
1. No of channels = 128
2. The signal is divided into nine segments
3. Number of emotions = 8
4. Number of samples per emotion = 50
5. Number of frequency bands = 6
I think, the following possibility
In hypothesis-1 comparisons were made among 128 electrodes hence, the multiple comparison procedure is applicable to 128x128 comparisons.
In hypothesis-2 comparisons were made across segments (9), emotions (8) and frequency bands (6). Hence, the multiple comparison procedure is applicable to 9*8*6 comparisons.
The other possibility is considering all the comparisons under one hypothesis s assuming that 128*128*9*8*6 comparisons are made (as pointed out by the reviewer of the manuscript)
Please suggest which possibility is appropriate given the data and hypothesis.
Relevant answer
Answer
Hi,
I think there needs to be a dimensional reduction in the 128 channel EEG output, region or lobe-wise. I think the segments already reduced it to nine dimensions. The other variables like Emotions and frequency bands cannot be further reduced. So, 9 segments X 8 emotions X 6 Freq. Bands would be ok.
Also for each of the variables, you require at least 8-10 cases to decrease the std. Dev, Examine the Std. Dev and Std. Errors and notice whether the 95% C.Is are narrow or not. If not then the sample size has to be increased or go for Non-Parametric statistics.
  • asked a question related to Segmentation
Question
4 answers
Can anyone tell me the open source image annotation tool for image segmentation?
Relevant answer
Answer
I will recommend Label Studio, it is a best and easy to use.
  • asked a question related to Segmentation
Question
5 answers
Is it a good idea to extract features from pre-trained, the last 1x1 convolution removed U-NET/Convolutional Autoencoder? Data will be similar and the model will be trained for image segmentation. I know everybody suggests freezing the encoder is the best option but I think there is feature extraction in the decoder part too(In both convolutional autoencoder and U-NET). They are high-level feature extractors, if my data was different, the frozen decoder part wouldn't be a good idea. But what if my data is very similar?
Relevant answer
Answer
An autoencoder is a neural network model that seeks to learn a compressed representation of an input. An autoencoder is a neural network that is trained to attempt to copy its input to its output.
Regards,
Shafagat
  • asked a question related to Segmentation
Question
3 answers
Hi
I am working with the UAV image data.
my study area is a dense forest.
How can I extract the dieback of the trees with deep learning techniques? do you know any package for this aim?
I want to extract the steps of the dieback trees.
thank you so much
Relevant answer
Answer
Hi dear Shafagat
Thank you for sharing the information and article.
I downloaded the article.
Good luck
  • asked a question related to Segmentation
Question
1 answer
Hello.
I have some CT scans of bones that have been handed to me and I need to segment.However the researchers that run the CT scannning process gave us .vol/.vgi files which are proprietary volume files.Is there anywhere to convert these stacks ( >2000 images) into a DICOM files ? The reason I want a DICOM files is because the cohort worked primarily with ITKSnap and that is what the software calls for.If not possible is there any alternative software that I can used to segment it from vol files (VGISTUDIO / SEG3D/ ... ) ? Any help would be welcome
Relevant answer
Answer
If they also give you the pcr (reconstruction parameters) file associated with the .vol file, you can use our little utility to import these files into open source 3D Slicer ecosystem.
  • asked a question related to Segmentation
Question
3 answers
Hello everyone! I am in search of a suitable dataset for the nail tracking application. I need a dataset, I found someone, but I want the images to be more variable. Please If you have one, response to my ask.
Relevant answer
Answer
Look the link, maybe useful.
Regards,
Shafagat
  • asked a question related to Segmentation
Question
2 answers
I am trying to develop an automatic segmentation system for T1 and T2 MRI (via Deep Learning) whose goal is to segment different areas of interest:
- Scalp
- Bones
- Blood vessels
- Cerebrospinal fluid
- White/gray matter
In order to be able to extract surfaces and to make calculations with.
At the beginning, I was based on an unsupervised segmentation system inspired by the W-NET model (https://arxiv.org/pdf/1711.08506.pdf).
But this system seems complicated to set up for this type of images. So I turned to other (supervised) models like U-NET or V-NET. But this kind of model requires to have the segmented mask as ground truth.
I would like to know if you have knowledge of the existence of a type of dataset where T1 and T2 brain MRI could already be segmented manually?
I found the following dataset: MRBrainS (https://github.com/looooongChen/MRBrainS-Brain-Segmentation) but it is only the brain that is segmented, not the whole head.
Thanks for your help!
  • asked a question related to Segmentation
Question
6 answers
how can I optimize the accuracy of the deep learning model for image segmentation by using methods optimization in python?
can anyone help me?
thank you in advance
Relevant answer
Answer
  • asked a question related to Segmentation
Question
1 answer
Im trying to simulate a Halbach Array in CST Studio, for wich I'd like to define each Cylinder Segment with a Permanent Magnet. Is there a clean way to seperate predefined segments from one another?
Relevant answer
Answer
Hi Tim
I do not know the answer to your question but suggest you can simulate your Halbach arrays in Maxwell. With this software, you will not face this problem. take a glance at this paper:
"Ship’s Magnetic Signatures Simulation Using Halbach Magnet Array as Uniform Static Magnetic Field Source"
or watch this video on youtube:
"Linear Halbach array - How to simulate it on Ansys Maxwell Software - Part 04"
  • asked a question related to Segmentation
Question
4 answers
Hello,
I am trying to perform an reverse transcription-PCR , where I capture the full-length of each Influenza B genome segment for a sequencing experiment. My plan is to do this in a one-pot RT-PCR for all segments. The terminal 10nt of each segment are identical thus my RT-PCR primer is designed to be exactly that 10nt, beyond those 10nt the sequence diverges between segments.
My question is, is a 10nt gene-specific primer too small (The Tm is 20 degrees) for an RT-PCR? As I know random hexanucleotide primers which are smaller and would have smaller Tms than my 10nt one, but those work just fine in RT-PCR.
The 10nt sequence isn't present anywhere else in the genome either.
Could someone advise if they belive this will work or not?
Relevant answer
Answer
What about multiplexing your initial RT (and or PCR)?
If you know the sequence net to the 10 most conserved bases already, you can multiplex for each segment, and even build in some degeneracies for known variants. A bit like this:
OR you do RT with tailed first strand synthesis primers (after the 10 conserved bases). It might be an option to do second strand synthesis with another adaptor using Template switching Reverse Transcriptase to ensure you go full-length at both 3' and 5' end..
  • asked a question related to Segmentation
Question
3 answers
For my research project, I generate some brain MRIs (T1w) and I have a recurrent issue with some non-zero voxels generated in the background. Note that generated images don't have skull. I would like to find a way or a tool for removing these artifacts. For example, I already tried with FSL-FAST, but all non-zero voxels are segmented as CSF even if they are clearly in the background. Maybe there exists some FSL-FAST options which may help me but I don’t find them…
Thanks in advance for your help.
Relevant answer
Answer
Hi,
maybe trying to run a despeckling filter to the images, removing features smaller than a certain amount of voxels?
  • asked a question related to Segmentation
Question
4 answers
In the field of medical imaging ,can we use U-net for segmentation, CNN for the feature extraction, and transfer learning based pre-trained alexnet, resnet, vggnet models for the classification.
Relevant answer
Answer
Mostly the first and best choice for image segmentation is U-net-based architectures. The following paper has reviewed U-net and its variation for medical image segmentation: U-Net and its variants for medical image segmentation: their...
A brief answer to your second question would be yes! CNNs can automatically extract existing patterns in an image which makes them perfect for feature extracting.
Lastly, it is so convenient to use pre-trained networks for classification. Even it may seem surprising when figuring out that in many medical papers, they use models pre-trained on ImageNet, which is totally irrelevant to medical images say MRI of the brain! In this case, they are benefiting from learning the basic patterns by the earlier layers.
  • asked a question related to Segmentation
Question
1 answer
I am experimenting with Retinal Optical coherence tomography. However, the region of interest named 'irf' has a very small area and I am using Dice loss for the segmentation in Unets.
However, I am not getting satisfactory results as the input images are noisy and also the ROI is very small. Can anyone suggest to me a suitable loss for this kind of challenge?
Relevant answer
Answer
  • asked a question related to Segmentation
Question
2 answers
Hello,
I am trying to do a Segmented regression in SPSS with knot/breakpoint estimates.
I have researched the resources online, but still can't figure it out. Any further reading or practical guidance on the steps to follow is mostly welcome.
Kind regards,
Natalia
Relevant answer
Answer
  • asked a question related to Segmentation
Question
1 answer
I'm currently analysing a data using conjoint analysis on the preferred online learning attributed of Senior High School Learners. Using cluster analysis (hierarchical) I was able to form clusters with considerable numbers of individuals. I wanted to determine the significance difference of the part-worth utilities and averaged scores between the segments. What Stat treatment should I utilise?
Relevant answer
Several methods to calculate significance in your case is given here:
Cluster analysis - Wikipedia
  • asked a question related to Segmentation
Question
1 answer
There are many dataset of epileptic patients before, during, and after seizures as preictal , ictal , postictal and interictal, all of which are related to brain signals. do you know a free Segmented dataset of the epileptic patient's heartbeat signal?
  • asked a question related to Segmentation
Question
1 answer
hello, does anyone familiar with molecular dynamic simulation of membrane protein using gromacs? i was learning of how to do it and was following tutorial KALP in DPPC. It was good until the end, so then I tried for other transmembrane protein. When doing shrinking using integro perl script, during energy minimalization step, it always stopped at 4th itteration with error of segmentation fault. Can anyone help? much appreciated
Error:
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
./shrink_bash.sh: line 25: 34251 Segmentation fault (core dumped) gmx mdrun -v -deffnm system_shrink${curr}_em
Before, 1st 2nd and 3rd itteration, there was a notice when performing em
" " "
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.
" " "
i assume there is something wrong with the em step. but i have no idea how to fix it.
I'll attach the pdb as well as the log
Relevant answer
Answer
I solved it by doing strong positional restrain to the whole protein. Because the only different is that hydrogen is also being restricted, maybe memory overload was caused by wierd hydrogen movement in unsolvated system?
  • asked a question related to Segmentation
Question
6 answers
Hello everyone,
here a few pictures of an anophthalmic aquatic insect, I am unable to identify.
It was found in a small brook and lives in fastflowing hygropetric environment. Region: Jura mountains, Switzerland, 860 m asl.
Dorso-ventrically flattened, no eyes, no antennae, six short legs, white patches on the edges of the dorsal segments, long thorns laterally on the ventral segments. Could be some coleoptera larva?
In advance many thanks for any suggestion.
Relevant answer
Answer
Nothing to add more than colleagues' opinion.
  • asked a question related to Segmentation
Question
4 answers
I'm working of DICOM images for the project I need multiple segmentation in one volume, anyone interested?
Relevant answer
Answer
Look the link, naybe useful.
Regards,
Shafagat
  • asked a question related to Segmentation
Question
4 answers
Hello,
I am currently writing my BA thesis and looking for some scientific sources about target group segmentation. Especially, Sinus Milieus, lifestlye orientated segmentation as well as so-called trend groups such as "LOHAS", "DINKs" and "Best Agers".
I am very thankful for any literature recommendations.
Thank you in advance.
Noemi
Relevant answer
Answer
You can refer inderscience or sage journals for relevant literature
  • asked a question related to Segmentation
Question
1 answer
Hi everyone,
I'm trying to apply the spatial interpolation process for my NetCDF file. However, I keep getting the "segmentation fault (core dumped)" error.
The screenshot of the error and my NetCDF file are in the attachment.
I'd be so glad if you could explain what goes wrong during the interpolation process.
Thanks in advance
Best of luck
Relevant answer
Answer
The problem seemed to be subregional cropping while downloading the climate data from Copernicus website.
  • asked a question related to Segmentation
Question
2 answers
Many scholars have discussed on the magma enhanced mechanism rifting (magmatic segmentation) of the Main Ethiopian Rift. But, research imputes are scares on the tectono-magmatic evolution of the MER in comparison with other global Mid Oceanic Ridge (MOR) zones.
Relevant answer
Answer
The tectonic nature of main Ethiopia rift is continental rifting due to up rising magmatic materials or convectional movement of molten material in the subsurface. The following paper entitled " Catching the Main Ethiopian Rift evolving towards plate divergence " which 2021 paper briefly discuss about the main Ethiopian rift . https://www.nature.com/articles/s41598-021-01259-6
  • asked a question related to Segmentation
Question
2 answers
Hello ,
I am working on a project that aims to segment automatically the subcortical brain structures on T1 weighted MR Images !
I started this project a few days ago and i am reading several papers and looking for different methods and algorithms that have been used to fulfill this task.
I would be pleased if someone that have worked on this kind of area on the brain to share with me papers and his/her feedback on what is the best way to do it !?
Anis.
Relevant answer
Answer
I don't know.
  • asked a question related to Segmentation
Question
5 answers
i am trying to solvate and neutralize a system containing more than 99,999 atoms (in my system an atom forms one residue) using VMD. however when i try to use psfgen to generate a segment for it, it only reads the first 10,000 atoms (residues) only.
attached is a file of the system.
How can i solve this problem?
Relevant answer
Answer
Within each segment/chain, every residue should have a unique identifier (columns 23-26), which is not the case -- hence the error.
  • asked a question related to Segmentation
Question
3 answers
I would like to generate the ground truth of text lines of handwritten document images to evaluate the accuracy of text line segmentation of these images. Could you please tell me if there is a free tool to define the text line of the handwritten document image?
Relevant answer
Answer
Try the sum of gradients for each line and next compare it.
  • asked a question related to Segmentation
Question
3 answers
I want to annotate medical images for segmentation to train a model. Some images may contain overlapping labels i.e. intersections of two or more labels in an area. The images are in png format. I've not yet found software (or I've missed) to create overlapping labels between areas. Which software is best to accomplish this task and how do I export the annotated image to masks?
Relevant answer
Answer
Hello sir…
I attached link; that talk about the best tool used for best labeling in image…
  • asked a question related to Segmentation
Question
3 answers
Reassortment is the result of segmentation phenomena, but why do some RNA viruses develope segmentation, not all RNA but especially groups of them with consideration of the segment number variation?
  • asked a question related to Segmentation
Question
3 answers
Error : forrtl: severe (174): SIGSEGV, segmentation fault occurred Image
I am trying to run MD in cloud, the following error has been encountered. Kindly help me to resolve the issue..
Relevant answer
Answer
Please, Pavan K Madasu , take a look at this Stack Overflow article describing how to properly create a reproducible example iwhen asking for help: https://stackoverflow.com/help/minimal-reproducible-example
Best
  • asked a question related to Segmentation
Question
5 answers
Hello Everyone, I am using ABAQUS & trying to simulate serrated chips while machining of Titanium alloy. But I am getting an error.
"An excessive temperature rate occurs in solving the heat transfer equations. This usually indicates that some elements are badly distorted or an error exists with model definition. You can check the temperature values and see if the distorted elements exist."
I am using ALE method. Any kind of suggestions will be highly appreciated.
Thank You
Relevant answer
Answer
Element deletion govened by J-C damage model.
  • asked a question related to Segmentation
Question
2 answers
I'm annotating CT scan slices from CQ-500 dataset with ITK-snap. One slice contains two labels(Subarachnoid and Intraparenchymal) in the same area. Here is the link: https://ibb.co/FJpyVZF
I'm trying to annotate this slice with ITK-snap. Since two labels are overlapping, the intersection area in the slice should contain both labels. But it shows it only contains the label which has been drawn last. Since the Subarachnoid area was drawn last over the Intraparenchymal area, the final segmented image only shows it contains Subarachnoid in the intersection region. I'm attaching the annotated slice (https://ibb.co/F3TrXtq) and segmented slice (https://ibb.co/sRgdndY) to clear my point.
What can I do to make the intersection area contain two labels? I'm new to ITK-Snap, so any help will be great.
Relevant answer
Answer
Thank you, Vikas Ramachandra . I have never done labeling with Pydicom, I will surely try it. I have solved my initial problem with 3DSlicer. Unfortunately, overlapping segmentation can only be done in 4D volume in 3dSlicer. I don't want to dive into 4D volume now, so I was thinking what if I create separate Nifti files for each separate label and train them in a 3D model (maybe U-Net). Would not that be okay? And what would be the appropriate loss function for this task as my dataset is very imbalanced?
  • asked a question related to Segmentation
Question
4 answers
I want to identify distinct consumer segments from my survey data. I have read articles using cluster analysis for consumer segmentation. Which method of clustering should I employ for the above analysis?
Relevant answer
Answer
Nidhi Joshi, to have done segmentation and clustering, you need to manipulate your data (and visualize it) in such a way that the clusters are more or less visible. Once done, apply k-means, mean-shift or other clustering algorithm.
  • asked a question related to Segmentation
Question
3 answers
Could anyone recommend a software that would help segment 3D MRI data sets of plant roots. I am currently working with ImageJ/Fuji and have played around with a number of the built in packages but haven't been able to produce the results I would like. Ideally I would like to extract information on root number, length, diameter and root volume in a (semi) automated way. Thanks in advance for any recommendations.
Relevant answer
Answer
Sent me an email and I'll introduce you to someone at UGA who does a lot of 3d root system modelling.
  • asked a question related to Segmentation
Question
5 answers
Hi everybody
Is there software to calculate IBDhalf and number of IBDhalf segments?
I appreciate your help.
Best regards
Relevant answer
Answer
Look the link, maybe useful.
Regards,
Shafagat
  • asked a question related to Segmentation
Question
6 answers
Hi there,
Myself and some collaborators were hoping to build a cell segmentation and morphology analysis tool using machine learning. I don't suppose any of you would be willing to share any images of cells from routine cell culture (or from experiments either works). Would obviously acknowledge you in the final publication should you wish to be.
Thanks!
Relevant answer
Answer
Look the link, maybe useful.
Regards,
Shafagat
  • asked a question related to Segmentation
Question
9 answers
I am working on human skin tone classification. For that I need to do skin segmentation. I am unable to find Compaq database and ECU's FSD database. If anyone has these database kindly help as I very much need them.
Relevant answer
Answer
Hi Priyansh, I’m currently doing skin detection. I wonder could you please share the Compaq and ECU datasets if you got any. Much appreciate! Priyansh Shah
  • asked a question related to Segmentation
Question
2 answers
I am currently trying to segment some fossil bones from their matrix in Dragonfly, but I am new to the software and am unsure what the best deep learning model architecture to use is. I am currently trying U-Net 3D, but I would like to know if there is a better one I should be working with.
Relevant answer
  • asked a question related to Segmentation
Question
5 answers
Hello everyone,
I am fairly new to cell culturing. For my experiments, I plate cells in 35 mm dishes. A crucial step in data analysis is cell-segmentation using the Stardist plug-in on ImageJ. However, I am struggling to obtain proper segmentation because all my cells tend to grow in clusters, making the segmentation processes highly unprecise.
To overcome this, when plating cells, I'd like to obtain single cells (similar to the image I attached.)
Does anybody have any suggestion on how this can be done?
I usually work with OVCAR cells.
Thank you in advance,
Giammarco
Relevant answer
Answer
Wash the cells with PBS without Ca2+/Mg2+ at the time of trypsinization and preferably use trypsin with EDTA. Clumps form because of the presence of free DNA in cell suspension which are released from dead cells. Free DNA attracts cells which bind altogether forming clusters.
You can use DNase I at concentrations from 20-100µg/ml to avoid formation of clusters. For each cell type, the working concentration must be determined individually.
Hope this is helpful.
Best.
  • asked a question related to Segmentation
Question
3 answers
Currently, I am working on a project that requires inference of instance segmentation on an Indian dataset. However, models like Mask-RCNN, pretrained on predominantly western images (like Fashionopedia or Modanet) cannot produce accurate segmentation performance.
So my question is that is there any open-source Indian fashion image dataset with available annotations for instance segmentation?
Relevant answer
Answer
Please understand the question first before answering. My question is very specific about an Indian fashion dataset, especially on the ethnic side. I can just google and find these links, but these are of no use when I am looking in a specific direction.
Thanks
  • asked a question related to Segmentation
Question
2 answers
I need help please
I have executed these commands to read the MRI images with extension nii:
[V,info]=ReadData3D;
imshow(squeeze(V(:,:,round(end/2))),[]);
I have run the code on the four module (T1, T1ce, T2, Flair) and also on the segmented images (ground truth). The black images still appear. For person number 1 (as an example), image 66 for this person, the resulting four non-segmented images are shown in attach, and they are not black. However, the resulting segmented image is completely black, why???
Where is the error in executing the code?
Regards,
Asmaa
Relevant answer
Answer
Hello
1. Change the image format.
2. Modify the modules.
3. If the image still encounters an error, you certainly did not observe a point in the defined code section, it will probably explain the reason for the error in the error section.
In the ([]) imshow field, set the resolution value range, put a number that may be so low that the image is completely dark, for example, write imshow (squeeze (V (:,:, round (end / 2))), [4000]).
  • asked a question related to Segmentation
Question
1 answer
Generally, In thermoplastic polyurethane elastomer (TPU), polydiol chains, known as soft segments and diisocyanate chains, called hard segments are arranged in a certain ratio. This hard and soft segment ratio in TPU governs its properties and application. Therefore, it is logical to determine the ratio of the hard and the soft segments in TPU.
Relevant answer
Answer
Dear Neeraj Mandlekar, normally the ratio is more or less the same as the one in the feed. Experimentally, it Can be calculated by characteristic elements via NMR and elemental analysis for example. Please have a look at the following documents. My Regards
  • asked a question related to Segmentation
Question
4 answers
I'm looking for a dataset of natural images, with no specific requirement on the type of scene, designed for the task of detecting (automatically or visually) the presence and position of small objects. This could come for example from an eye-tracking experiment where participants are tasked to e.g. look for dogs in a picture taken with a camera, or an image segmentation dataset. The point is that the task is challenging/the category is rare/the segmentation area is small and hard to find. Each scene would ideally be associated to a label or set of labels indicating the object/s to be searched for, an explicit position or the segmentation masks are a plus but not required.
Relevant answer
Answer
Mask COCO dataset
  • asked a question related to Segmentation
Question
9 answers
Open source softwares
-3D Forest
Comercial softwares
-Liforest
-EnviLidar
Relevant answer
Answer
Hi ! In addition to the above you can see: R packages: 1. TreeLS (https://github.com/tiagodc/TreeLS) 2. rTLS (https://github.com/Antguz/rTLS) 3. lidR ( https://github.com/r-lidar/lidR) is a package mainly for ALS, but you will find there many algorithms useful in TLS tree segmentation, so you can write your own workflow Python: 4. FSCT (https://github.com/SKrisanski/FSCT) 5. treeseg (https://github.com/apburt/treeseg) Standalone applications: 6. DendroCloud (http://gis.tuzvo.sk/dendrocloud/) 7. SSSC (https://github.com/dwang520/SSSC) - it is also possible to run algorithms via Matlab (maybe Octave). You can also find a short section about forestry TLS software in my article, there you can find a bit more information about the functionalities of this software
: If you (or anyone else) have any questions or are interested in collaborating on forestry TLS topics, please feel free to contact me.
Best regards,
Grzegorz Krok
  • asked a question related to Segmentation
Question
6 answers
I need a clear step wise explanation of the inner workings of the YOLO deep learning segmentation model with all the mathematical nuances.
Relevant answer
Answer
YOLO is a clever convolutional neural network (CNN) for doing object detection in real-time. With YOLO, a single CNN simultaneously predicts multiple bounding boxes and class probabilities for those boxes. YOLO trains on full images and directly optimizes detection performance. YOLO algorithm is an algorithm based on regression, instead of selecting the interesting part of an Image, it predicts classes and bounding boxes for the whole image in one run of the Algorithm. Ultimately, we aim to predict a class of an object and the bounding box specifying object location. Image segmentation is the task of clustering parts of an image together that belong to the same object class. This process is also called pixel-level classification. In other words, it involves partitioning images (or video frames) into multiple segments or objects.
Also, kindly check these papers:
  • asked a question related to Segmentation
Question
6 answers
Do the traditional methods of segmentation, targeting, and positioning anchored to economic criteria, such as per capita income or standard of living are still relevant? or marketers should segment markets on the basis of their social media behavior?
Relevant answer
Answer
The practice of breaking down and categorizing your target audiences based on shared features like as demographic information, behavioral patterns, and geographic location is known as social media segmentation. This makes it simpler to design adverts that are more tailored to a certain audience's interests.
The four primary categories of market segmentation are demographic, psychographic, behavioral, and geographic segmentation, although there are many additional tactics you may apply, including several variants on the four main types. Here are a few more options for you to consider.
Marketers can segment clients based on their engagements with their brand, such as purchase history and online interactions. They may also track consumer lifecycle activities such as getting married, having a baby, or purchasing a home, as well as seasonal spending habits such as Christmas shopping.
  • asked a question related to Segmentation
Question
7 answers
Hello
Dear researchers,
Which neural network ( ResNet or UNet) do you suggest if the input data of the model is the image-based data and the purpose of the model is classification? Why?
If the goal is segmentation with image-based data, then which deep neural network(Resnet or U net) do you suggest for the predictive model? Why?
My focus is just two deep neural networks such as ResNet or UNet
Thank you for your guidance
I am waiting for your guidance
Relevant answer
Answer
Thanks for asking this good question. In my case study, UNet performed better than VGG16, VGG19 and ResNet. Actually, UNet is "a convolutional neural network architecture that expanded with few changes in the CNN architecture".
  • asked a question related to Segmentation
Question
5 answers
I have downloaded the raw pancreas-CT dataset (that has a DICOM file extension) from wikicancerimagingarchive.net and want to use it on Google Colab by loading it for segmentation. My downloaded data has 3 sub-folders for each folder in the Pancreas-CT dataset folder even before the content is seen. I am having a challenge dividing them into training, validation (and testing) and I shall be greatful if anyone can help.
Relevant answer
Answer
Isaac Baffour Senkyire, yes, dear, it shows the same with me, and I don't know how to deal with this. if I find a solution, I will let you know
  • asked a question related to Segmentation
Question
1 answer
if medico-legal case comes with fractured tooth segment or avulsed tooth, then how to determine time period or time duration of injury/assault clinically or histologically?
Relevant answer
بحسب مرونة السن
  • asked a question related to Segmentation
Question
5 answers
I would appreciate discussing and exploring the latest research gaps in Brain Tumor Segmentation and Classification.
  • asked a question related to Segmentation
Question
6 answers
Network segmentation reduces attack surface by blocking an attacker in a certain portion of the network. How can I measure the reduction of attack surface after applying segmentation either mathematically or through simulation? Much appreciate your suggestions. Thanks
Relevant answer
Answer
You can achieve your goal by using Gns 3 simulation and MATLAP
  • asked a question related to Segmentation
Question
4 answers
Hello dear researchers
How to do the watershed algorithm in eCognition developer software?
Do I need to add a plugin to watershed segmentation? How? There is no watershed segmentation plugin in my software.
Thank you all
Relevant answer
Answer
The algorithm works on a gray scale image. During the successive flooding of the grey value relief, watersheds with adjacent catchment basins are constructed. ... A set of markers, pixels where the flooding shall start, are chosen. Each is given a different label.
Regards,
Shafagat
  • asked a question related to Segmentation
Question
5 answers
I have a dataset and I intend to use multi-label learning approach to recognize the various objects present in the images dataset. What is/are the appropriate segmentation approach to use for the multiple objects detection task?
Relevant answer
Answer
Multi-label classification involves predicting zero or more class labels. Unlike normal classification tasks where class labels are mutually exclusive, multi-label classification requires specialized machine learning algorithms that support predicting multiple mutually non-exclusive classes or “labels.”
Regards,
Shafagat
  • asked a question related to Segmentation
Question
4 answers
Hi,
I am new to EEGLAB, and I have an issue with the CleanLine package. I have some epoched recordings with flat periods. During the pre-processing, I observed that CleanLine reduces the line noise very well, but it introduces previously non-existing noise in the flat period. These periods are not a problem because I can reject them, but after CleanLine, also the time around the flat segment becomes noisy. This happens even when I reject the flat segment before performing the CleanLine.
Has anybody had the same issue? Do you know how to fix it without losing data?
I really appreciate any help you can provide.
Ana
Relevant answer
Answer
Is this a new installation? Is anything else plugged into the same wall power outlet? And you may need an "Isolation Transformer". In the US this is on Amazon: Tripp-Lite-Isolation-Transformer-Outlet ~ 100 euros.
You would need to find an EU versions.
  • asked a question related to Segmentation
Question
5 answers
I build an predictive machine learning model that generate the probability to default over the next 2 years for all the companies in a specific country. I used for training the algorithms financial data for all these companies and also the NACE codes (domains of activity) and I'm wondering if I will develop a better model if I somehow segment the population of B2B in segments and run distinct models on these segments.
Hope you can advice!
Lots of thanks in advance!
Relevant answer
Answer
You can work on different aspects starting as cited A demographic approach and it could be also a geographic one depending on what information the dataset includes also you can try to identify behavioral patterns within your data. Also, you could go further by focusing on Customer capabilities & the Nature of the existing relationships.
  • asked a question related to Segmentation
Question
3 answers
I am trying to classify apnea and non_apnea ECG segments (for sleep apnea detection) of "Apnea_ECG" dataset. To test the algorithm, I need apnea annotations for testing set (x01-x35) and, the file for apnea annotations for testing set in not available at physionet.org. Suggest the way to get annotations for testing set.
Relevant answer
Answer
Hello, is there an archive for the rest of he signals a01 to C10? Thank you!
  • asked a question related to Segmentation
Question
2 answers
What are some articles in which this technique was appropriately/well applied and reported?
  • asked a question related to Segmentation
Question
3 answers
Could You please give me a link to a source where I can get (for free) a data set of contrasted CT images of an abdominal aortic aneurism in DICOM (or which?) format manually segmented by a specialist? Even a normal abdominal aorta will fit.
Relevant answer
Answer
Hi,
This article may be useful to you
  • asked a question related to Segmentation
Question
6 answers
How feasible it is to classify cancer images without segmenting out the nuclei.? I am not talking about deep learning algorithms but classification using ANN, SVM etc. If we classify the images, how features extracted??
Relevant answer
  • asked a question related to Segmentation
Question
1 answer
I have an endocast that I am trying to measure the volume of the olfactory bulbs from. I have the data segmented in Avizo, but unfortunately because of the way the specimen was scanned (it was a fluid specimen) the skull was not in anatomical view when it was CT scanned. As a result, it is very difficult to determine where the borders of the olfactory bulbs are.
I am trying to reorient the segmented data so I can get it in standard anatomical view for further analysis, specifically resegmenting the label field to define the olfactory bulbs separately. I know that it is possible to resegment the CT data in Avizo, but I am trying to avoid this as I know it can cause issues with blurring of boundaries between bone and tissue. I was wondering if there is any way to do this with a segmented label field, isosurface, or other data that has already been segmented and thus the anatomy is better defined.
Relevant answer
Answer
Hi Russell,
in Amira-Avizo, you can use the Transform Editor of any data-object to change its orientation and position in the global coordinate system.
So, you could use the Transform Editor of your segmented data to rotate it as needed, and afterwards you can use Resample Transformed Image to get get an axes-aligned voxel-grid. (see attached "TransformEditor_snapshot.PNG")
I don't know your workflow, but maybe you could also use the 3D lasso-tool in the Segmentation Editor to select an arbitrarily oriented part of one material and assign that to a new material (see attached screenshot "SegEdit_snapshot.PNG").
For making the selection working only on one specific material, you have to "lock" the other materials appropriately. Remember, you have the "undo" with <Ctrl>+Z ...
There might be some issues with the update of the visualisation when using the 3D-lasso, so it might be necessary to toggle off/on the 3D-view of a material.
Kind regards,
Andreas
  • asked a question related to Segmentation
Question
1 answer
Qamchuqa formation represent forebulge depozone of zagrose foreland basin. Iraq 🇮🇶 segment.
Relevant answer
Answer
The Qamchuqa formation is a formation or a well exposed which located in northeast of Iraq which contains thick reservoir units in high folded zone.
  • asked a question related to Segmentation
Question
6 answers
Deal All,
I have two series of time series data that I would to correlate. One data set is the deposits, by month, for a list of different account. The other is the balances, by month, for the same list of accounts. In essence, I have two matrices that I want to understand correlation for without having to strip out each account separately. Furthermore, I want to cross-section that data into different segments.
This is being done with the goal of being able to forecast account balances in the futures, by looking at their usage behavior (assuming there is a lag relationship).
How do I build an intermediate matrix of the correlations? Is there a way to do it in Python or R-Studio? Is there a way to do it in excel?
Thanks
Ryan
  • asked a question related to Segmentation
Question
9 answers
Hello everyone,
Can anyone suggest interesting books/documents/papers on segmentation techniques especially on medical imaging?
Best Regards
Relevant answer
Answer
  • asked a question related to Segmentation
Question
19 answers
Hi. I'm working on 1000 images of 256x256 dimensions. For segmenting I'm using segnet, unet and deeplabv3 layers. when I trained my algorithms it takes nearly 10 hours of training. I'm using 8GB RAM with a 256GB SSD laptop and MATLAB software for coding. Is there any possibility to speed up training without GPU?
  • asked a question related to Segmentation
Question
3 answers
I'm looking for a dataset containing ultrasound images with tools (e.g. needles or catheters) and their segmentations. I want to train a CNN to perform the segmentation
Relevant answer
Answer
  • asked a question related to Segmentation
Question
31 answers
Dear friends,
We invite all researchers and practitioners who are developing algorithms, systems, and applications, to share their results, ideas, and experiences.
Topics of interest include, but are not limited to, the following:
Hybrid Metaheuristics
Theoretical aspects of hybridization
Automated parameter tuning
Parallelization
Evolutionary Computation Algorithms
Swarm Optimization
Multi-objective optimization
Multilevel segmentation
Object recognition
Computer vision
Image processing
Filtering and enhancement
Morphology
Edge detection and segmentation
Feature extraction
Quantum Image Processing
Image thresholding
Applications
Relevant answer
Answer
Prof. Diego Oliva: Yes, with pleasure. Thank you for this useful information.
  • asked a question related to Segmentation
Question
3 answers
I have done PCA analysis of DNA ligand complex But it gives error diagonalizing segmentation fault core dumped.
with this command-
gmx covar -s ref.pdb -f md1_backbone.xtc
Relevant answer
Answer
Follow these steps:
  1. What I usually use as the measure of reconstruction error (in the context of PCA, but also other methods) is the coefficient of determination R2 and the Root Mean Squared Error (or normalised RMSE). ...
  2. The R2 of the ith variable can be computed as:
  3. R2i=1−∑nj=1(Xj,i−fj,i)2∑nj=1X2j,i.
Kind Regards
Qamar Ul Islam