Python Programming for Biology: Bioinformatics and Beyond

Figure 18.5 (Plate 8).  Images from micrograph cell-counting procedure. An original

microscope image of mammalian cells is shown alongside the results of the edge detection

and a greyscale version where the different cell-edge features are labelled with colours

after blob analysis. Isolated cells are yellow, overlapping cells are blue and small

fragments are red.

1

 As  of  2013,  PIL  has  not  been  ported  to  Python  3,  but  an  alternative  implementation,

Pillow, has been:

http://python-imaging.github.io

.

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2

http://www.imagemagick.org/

.

3

Download PIL via links at

http://www.cambridge.org/pythonforbiology

.

4

 These  Image  objects  sometimes  cause  problems  if  they  are  associated  with  a  local

variable,  e.g.  inside  a  function,  and  get  garbage  collected  sooner  than  expected.  If  this

occurs then the general solution is to make sure that the image object has a reference from

another object that will persist in memory, for example by putting it in a non-local list or

adding it as a self. attribute.