Content

Cytogenetic

• Highlighting Interstitial Telomeric Spots : HITS-FISH
• FISH calibration

Molecular biology

• Possible detection of telomeric fusions by PCR

Datasets

MFISH

• ADIR  MFISH images (multispectral dataset)
• Making a MFISH image (numpy)
• Making a MFISH image with scikits.image
• MFISH image to RGB with image5D

Overlapping chromosomes

• Generating synthetic images of overlapping chromosomes 
• DeepFish github repo 
• Sy,thetic 82146 low res images of overlapping chromosomes 
• Modeling overlapping pairs of chromosomes: a dataset containing more than 200 000 pairs of images in png format.
   
• 100 overlapping, full resolution, chromosomes isolated from 14 metaphases of human lymphocytes

Modeling Telomeres in-silico

• Modeling the Telomere length distribution with Chromosomal Segregation along Synchronous Cellular Divisions

Python libraries  

Deep learning

• Building tensorflow 1.10 from source on ubuntu 16.04 (old Xeon CPU issue) 
• Using tensorflow 0.7 on a laptop (Manjaro linux) 

Mathematical morphology

• Building YaYi under Ubuntu
• Buiding Mamba under Ubuntu
• mahotas : example
• pymorph: example
• PINK  "Most of the operators come from mathematical morphology, but it contains operators from different fields."

More general image processing library:

• scikits-image: example MFISH image
• cv2:loading a 12 bits image
• Buiding opencv 2.4.2 for Ubuntu 12.04

Image processing

Chromatids segmentation:

• Painting chromatids "by hand" with ImageJ
• Watershed for chromatids  labelling  with hand chosen seeds
• Seeds exploration  (watershed)
• Chromosomes skeleton extraction with ImageJ
• Paired seeds could label chromatids

Metaphase segmentation

• With ImageJ
• Segmentation I (python+pymorph)
• Segmentation II (python+mahotas+pymorph)

QFISH on nuclei

• Telomeric spots quantification in a nucleus

Chromosomes segmentation:

• Resolving overlapping chromosomes: an emblematic case

• Particles extraction : toy model.
• DAPI stained chromosomes extraction
• Detecting end points or branched points from the skeleton of a single chromosome
  
   

2D Shape analysis

• Selecting a maximal area quadrilateral from four random points 
  Simple direct quadrilaterals found with the shoelace formula 
• Resolving overlapping chromosomes: an emblematic case

Skeleton, edge and graph

• Detecting end points in a skeleton
• Detecting end points or branched points from the skeleton of a single chromosome
• Detecting branched points in a skeleton
• Hit or miss: skeleton and convex hull with Python 
• Which structuring elements to detect branched points?

• Converting an open curve to a list of ordered pixels: a python test code
• open curve to ordered pixels: a second test 
• Closed curve to set of ordered pixels: a python test 
• Computing the convex hull area of a 2D binary particle

• Analysis of the orientation of a particle by erosion
• How to rotate faster chromosomes vertically (a little bit) 

• Neighborhood in a labelled image
• Getting the neighborhood of labelled particles in a graph

•  An endpoints spectrum:possible features from the skeleton? 

•  From binary image skeleton to networkx graph

• Graph pruning (graph-tools lib)
• Issue when trying to convert a binary skeleton into a networkx multigraph 

Data processing, Classification

•  Chromosomal shapes classification by Linear Discriminant Analysis with R

• chromosome classification:workflow
• chromosomes, overlapping chromosomes and nuclei:data processing with pandas
• Classifying chromosomes with scikit-learn

GUI

GUI:Matplotlib, Pylab issues

• Matplotlib subplot I
• Pig chromosomes gallery
• gallery with size filtering

GUI:pygame

• pygame for  karyotyping?
• this is not a karyotyper
• toward classification: sprite, drag and drop
• sprite and rotation
• Classifying chromosomes (overlapping or not), nuclei, dusts.
• Moving chromosomes with kivy
   

GUI: pyQT4 (and xml)

• using a xml tree to make an images database?
• A pyQt4 GUI and a xml file
• Reordering ADIR MFISH images with python scripts
• Playing with the ADIR mutispectral images database
• FlyFISH : navigation into an images database based on xml
   

Hardware

• Frankencomputer for deep learning: running ubuntu 16.04 on a Dell Precision T5500