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Dear all,

This is the third and last HW assignment for this semester.

It deals with graph theory and digital images.

Since we will soon begin working on the projects, please start working on this HW soon, so you can free you mind (and time) for the projects.

Have a nice weekend,

Amir

HW3 (last!) is online by Amir RubinsteinAmir Rubinstein, 11 May 2017 15:39

Dear all,

The second reading assignment is now online.
It is about images processing - a rather fun topic and very useful in biological context.

Due date is 9th of May - class time.

In addition, because HW2 is currently due at a vacation day, it is postponed to a week later, May 9th (23:55).

Cheers,

Amir

HW2 is online
Amir RubinsteinAmir Rubinstein 18 Apr 2017 16:32
in discussion News / News - 2017 » HW2 is online

Good luck,
Amir and Gur

HW2 is online by Amir RubinsteinAmir Rubinstein, 18 Apr 2017 16:32
HW1 is online
Amir RubinsteinAmir Rubinstein 28 Mar 2017 17:31
in discussion News / News - 2017 » HW1 is online

Dear all,
Please read the instructions on page 1 of the HW carefully.
Students who participated in today's class are exempt from submitting Q3, except for section d. In this section you are required to provide a short discussion on the results we saw in class. I encourage you to play a bit with the code and execute it on additional genes, through which you may get additional insights.
The deadline of HW1 was set to April 11, which is Passover evening, so it is postponed to April 13.

Regards,

The course staff

HW1 is online by Amir RubinsteinAmir Rubinstein, 28 Mar 2017 17:31
Welcome!
Amir RubinsteinAmir Rubinstein 22 Mar 2017 07:52
in discussion News / News - 2017 » Welcome!

Dear students,

Welcome to "Computational Approaches for Life Scientists", Spring 2017.
The first reading assignment is online, due until next class.

Good luck,
The course staff

Welcome! by Amir RubinsteinAmir Rubinstein, 22 Mar 2017 07:52

Hello all,

A reminder that the date is August 4th.

Also, I uploaded a short survey to moodle, which I ask you to fill.

the feedback is very important for me.

Good luck all,

Amir

shira atilli (guest) 19 Jun 2016 19:18
in discussion Q&A and discussions / Spring 2016 » Refreshments for the last meeting

I will bring croissants.

by shira atilli (guest), 19 Jun 2016 19:18
Amir RubinsteinAmir Rubinstein 18 Jun 2016 20:35
in discussion Q&A and discussions / Spring 2016 » Q&A

convert is a method of PIL images.
So I think you should first convert the ndarray to image.

by Amir RubinsteinAmir Rubinstein, 18 Jun 2016 20:35
Shilo Ohayon (guest) 18 Jun 2016 16:45
in discussion Q&A and discussions / Spring 2016 » Refreshments for the last meeting

I will bring cookies and a snack

by Shilo Ohayon (guest), 18 Jun 2016 16:45
Shirane Tsedef (guest) 18 Jun 2016 16:14
in discussion Q&A and discussions / Spring 2016 » Q&A

Hey,

I have a problem with converting a nd.array into a figure.

The code is:

sobely = cv2.Sobel(img,cv2.CV_64F,0,1,ksize=5) ### type(sobely)=nd.array

if not os.path.exists('./CONVERT/'):
os.makedirs('./CONVERT/')

sobely_img = Image.fromarray(sobely)
sobely_img.save("./CONVERT/sobely.jpg")

and I got an error message:
OSError: cannot write mode F as JPEG

I tried to write it like this:
sobely = cv2.Sobel(img,cv2.CV_64F,0,1,ksize=5).convert("L")

and I got the error:
AttributeError: 'numpy.ndarray' object has no attribute 'convert'

Does anyone know what can I do??

by Shirane Tsedef (guest), 18 Jun 2016 16:14
Noga Zur (guest) 18 Jun 2016 15:12
in discussion Q&A and discussions / Spring 2016 » Refreshments for the last meeting

I will bring a bottel of drink and a snack

by Noga Zur (guest), 18 Jun 2016 15:12
Eden Cohen (guest) 18 Jun 2016 14:20
in discussion Q&A and discussions / Spring 2016 » Refreshments for the last meeting

I will bring disposable plates and a snack

by Eden Cohen (guest), 18 Jun 2016 14:20
Shirane Tsedef (guest) 18 Jun 2016 14:15
in discussion Q&A and discussions / Spring 2016 » Refreshments for the last meeting

I will bring little vegan desserts! :)

by Shirane Tsedef (guest), 18 Jun 2016 14:15
Shiran Sarig (guest) 18 Jun 2016 13:55
in discussion Q&A and discussions / Spring 2016 » Refreshments for the last meeting

I will bring disposable cups and bamba

by Shiran Sarig (guest), 18 Jun 2016 13:55
Ziv & Dina (guest) 18 Jun 2016 13:47
in discussion Q&A and discussions / Spring 2016 » Refreshments for the last meeting

we will bring "shtoochim", cookies and two bottles of soft drink.

by Ziv & Dina (guest), 18 Jun 2016 13:47

I will bring vegan chocolate chip cookies.
If you want to bring some refreshments / drinks pls post below.

Qian (guest) 19 May 2016 13:59
in discussion Q&A and discussions / Spring 2016 » Q&A

Uninstall python 3.5.1 and re-install it, not need to change to 3.4.

I did it for 64 bit windows and then Pillow worked.

by Qian (guest), 19 May 2016 13:59

The image we used for labeling demonstration in class was taken from this website: http://www.broadinstitute.org/bbbc/image_sets.html. It contains many image sets that can be used to test image processing algorithms.

The specific image we used is from the data set called BBBC004 (http://www.broadinstitute.org/bbbc/BBBC004), which contains synthetic images. There are several sets, and I chose the one with overlap probability = 0, the file named 1GRAY.tif.

Since this is a synthetically generated image, the "ground truth" mentioned on the site is accurate: exactly 300 cells.

WhatsApp-Image-20160518_.jpg

So, we have a winner in our competition - well done Omer!

I remind you that next week there is no class, Tuesday is acting as a Thursday.

Amir

eden (guest) 16 May 2016 21:01
in discussion Q&A and discussions / Spring 2016 » Q&A

עובד, תודה!

by eden (guest), 16 May 2016 21:01
Amir RubinsteinAmir Rubinstein 16 May 2016 12:39
in discussion Q&A and discussions / Spring 2016 » Q&A

The easiest solution would be to install Python 3.4 (uninstall 3.5 before), and then follow the link from the slides.
Amir

by Amir RubinsteinAmir Rubinstein, 16 May 2016 12:39
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