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nuclei Key Features
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Community Discussions
Trending Discussions on nuclei
QUESTION
I am using this borrowed code to automatically count DAPI stained nuclei.
...ANSWER
Answered 2021-Feb-25 at 05:42I thought MATLAB's imfindcircles
might be useful here. It overcounts #14, but seems to do better than what you have right now.
QUESTION
I am using PanNuke: An Open Pan-Cancer Histology Dataset for Nuclei Instance Segmentation and Classification
Here I have found masks.npy
, an array of approximately 10 GB, shape (2656, 256, 256, 6). Now I want to explore it to look inside data. How can I do this?
Here is the code:
...ANSWER
Answered 2020-Oct-11 at 02:33Since you are new in python, the first procedure is understand your dataset. For this multidimentional array 2656 is the number of records in the array (2656 mesurements). 256 and 256 Are two dimensions to draw the image (like numerical values for pixels in some squared picture). And the last dimension: 6, defines nuclei classification: Epithelial, Inflam, Malignat, Necrotic, Str, Non-nuclei.
There is more than one way to have the insights for this dataset (numerical and graphical), to learn how to deal with biomedical images you could try this: https://learn.datacamp.com/courses/biomedical-image-analysis-in-python
QUESTION
There are 16 invalid values in the dataset. How can I detect and delete rows with these invalid values? Does it make more sense to mean or mode rather than delete the row of data?
...ANSWER
Answered 2020-Sep-05 at 22:03Let's say you want to remove all rows with 'Cell-Size' below zero. This will do that:
QUESTION
I am writing a program to simulate radioactive decay. I am using a class with a decay_sim
method which generates a 2D numpy
array with ones (not decayed) and zeros (decayed) called self.nuclei
. It is a pseudo-random process, so the array is different each time. I then use a visual
method to plot this array as a colour grid using matplotlib
.
This is an example of the self.nuclei
array:
ANSWER
Answered 2020-Aug-17 at 18:58You can create a custom legend from rectangular patches. The colors for the mesh can be set via LinearSegmentedColormap.from_list()
.
QUESTION
In a SLURM cluster I am submitting a shell script that calls a python script (both scripts can be found below. When the shell script executes it get until where the python script is called but then nothing happens: there is no output, no error message and the SLURM job keeps running.
I assume the entire contents of the python script are not relevant (but I included it anyway for completion). For debugging purposes I inserted the print("script started")
line at the very beginning to see if it gets run but it doesn't. The last thing I see in the output is moved to directory
.
I tried calling a test.py
script containing print("test")
right before this and it gets executed normally.
What could be the reason the python script doesn't start and how can I fix it?
Edit: As user jakub recommended changing print("script started")
to print("script started", flush=True)
successfully gets printed. Including several more of these statements revealed that the script was actually running perfectly fine, it just didn't output anything. Including the same statement within the for loop that gets constantly executed also makes all print()
statements previously missing get printed.
The question then turns into: why do the print()
statements here need to have flush=True
in this script but not in other scripts?
Shell script:
...ANSWER
Answered 2020-Aug-15 at 12:34Python buffers stdin, stdout, and stderr by default. print()
writes to stdout
by default, so you will see this buffered behavior.
From https://stackoverflow.com/a/14258511/5666087 :
Python opens the stdin, -out and -error streams in a buffered mode; it'll read or write in larger chunks, keeping data in memory until a threshold is reached.
You can forcibly flush this buffer by passing flush=True
to print
. See the documentation for more information. If you have multiple print
statements in a row, you need only use flush=True
in the last one.
QUESTION
The libraries I'm using are:
...ANSWER
Answered 2020-Aug-13 at 17:53Here is a script to clean the column. Note you may want to add more words to the stopword set to meet your requirements.
QUESTION
Two entities with a onetoone relation First one is a table Second one is a view
Nuclei
...ANSWER
Answered 2020-Jun-26 at 13:32Axiom: Everything is difficult until you understand it.
Our first need is to understand how this works. In PHP, private
/protected
means they will not be available outside the object's scope. Twig tries to access them from outside the object scope, which causes the problem.
In other words: What your Twig attempts to use is not available to it.
Yet, I'm sure you have seen Twig seemingly using private
/protected
members, so your empiric evidence seemingly contradicts to the theory I have outlined. But only seemingly. You understand what the problem is, but at this point you don't yet understand how those keywords can be used.
The documentation is clear about it, when it explains that when foo.bar is being used, if bar is not a member of foo, then it eventually checks for foo.getBar(), a getter. So, you will need to implement getStatistiche
and operate similarly for its members. I did not use Twig for a while, but if memory serves me well, for totale_conferimenti
you will need getTotaleConferimenti
.
EDIT (Jakumi's helpful comment):
you're about 90% right. Symfony usually assumes camel case and in that case your assumed getter name would be correct. the error message states the expected getter name though. also additional handy information: dump's output has a - prepended to every private/inaccessible property and + prepended for every public property. The diagnosis however is a 100% correct, missing getter for an "inaccessible" property and no possible fallback.
QUESTION
I looked around and found no answer that supports n
number of tables in one page where each table has its own filter, sort and pagination.
On https://material.angular.io/ they have given an example of one table for a page.
This is what I've written for one table-
HTML
...ANSWER
Answered 2020-Jun-23 at 17:20You're going to need to use @ViewChildren
instead of @ViewChild
and make use of QueryList
to read childrens effectively.
You'll also need ngAfterViewInit()
once the initialization of a component's view is completed to update paginator and sort.
Please read between the lines for comments.
TS
QUESTION
Two tables Utenti and Nuclei related each other
Utenti SQL
...ANSWER
Answered 2020-Jun-23 at 15:00Remove line:
QUESTION
I'm working on a nuclear segmentation problem where I'm trying to identify the positions of nuclei in images of stained tissues. The given training dataset has a picture of the stained tissue and a mask with the nuclei positions. Since the dataset was small, I wanted to try data augmentation in PyTorch, but after doing that, for some reason, when I output my mask image, it looks fine, but the corresponding tissue image is incorrect.
All my training images are in X_train
with shape (128, 128, 3)
, the corresponding masks in Y_train
with shape (128, 128, 1)
and similarly the cross-validation images and masks in X_val
and Y_val
respectively.
Y_train
and Y_val
have dtype = np.bool
, X_train
and X_val
have dtype = np.uint8
.
Before data augmentation, I check my images like this:
...ANSWER
Answered 2020-May-20 at 00:28You are converting the images to PyTorch tensors, and in PyTorch the images have size [C, H, W]. When you are visualising them, you are converting the tensors back to NumPy arrays, where images have size [H, W, C]. Therefore you are trying to rearrange the dimensions, but you are using torch.reshape
, which doesn't swap the dimensions, but only partitions the data in a different way.
An example makes this clearer:
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Rust is installed and managed by the rustup tool. Rust has a 6-week rapid release process and supports a great number of platforms, so there are many builds of Rust available at any time. Please refer rust-lang.org for more information.
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