yeast-spotifier 1.2.1

a script to process yeast plate image into figures

Spotifier

This script to covert pre-processed plate images into figures.

Nothing fancy at the moment, no deep learning segmentation ;-) the script works using plates spotted according to provided template. Still, this helps to get this task done quicker!

! Download a set of templates for copper plates https://github.com/mmagnus/yeast-spotifier/releases/download/v1.0/templates-for-copper-plates.zip !

Table of Contents

• Spotifier
  • Options
  • Prepare image
  • Adjust the image to the template
  • Prepare mapping file
• Customization
• Mappings
• For reporters
• Digitifier
• Install
• Changelog

Created by gh-md-toc

Options

usage: spotifier.py [-h] [-v] [-d] [--align] [-x X] [-y Y]
		    [--trim-rms TRIM_RMS] [--size SIZE] [-a]
		    map file [file ...]

install to work on psd files: psd-tools3

positional arguments:
  map                  map
  file                 pre-processed image(s)

optional arguments:
  -h, --help           show this help message and exit
  -v, --verbose        be verbose
  -d, --debug          be even more verbose
  --align              align dots
  -x X
  -y Y
  --trim-rms TRIM_RMS
  --size SIZE
  -a, --dont-annotate

Fig. -t, trim background to get nicely formatted dots.

Prepare image

Open the image:

Image -> Adjustments -> Black & white OR cmd+alt+shift+b

Inverse color (cmd+i)

Adjust Levels (cmd+l), select black backgroud with the black pippette and white for the white pippette.

Crop image and Edit -> Image Rotation -> Flip Canvas Horizontal.

Adjust the image to the template

Open template.psd and drag and drop plate photo

Lower opacity for the imported image, to around 30%, to see the template in the background.

Use Move tool and Free transform fit the image to the template.

Use Move tool and Free transform to move "Rectangle" to cover the plate.

Switch off the Backgroud layer, set Opacity to 100.

Save as a PSD (or jpeg) file, e.g., s02_30.jpeg.

Prepare mapping file

Open a text editor and prepare a file used to map dots into figure.

Run the program:

python spotifier.py testdata/02/s02_30.psd -t -m testdata/02/map.txt

The results should be like this:

and the file s02_30_spots.png should be created in the folder next to the input file (in this case testdata/s02/s02_30_spots.png)

---

TIP: If you want to introduce one extra, empty line, just add an empty line to a map file.

Customization

If you want to move single dots, use Preview and just move them around, save it (if you open a JPG, you will be asked if you want to convert the file to PNG, yeah, do it, remember only to change the file name in the command, 18_X.png).

and re-run:

python spotifier.py testdata/02/18_X.png -t -m testdata/02/map.txt

---

Use play with Opacity to see Backgound with the template to adjust positions of your dosts.

Mappings

Some ideas for your plates ;-):

5, 6, 7
8, 9, 10

12, 13, 14
15, 16, 17

20, 21, 22
23, 24, 25

28, 29, 30
31, 32, 33

36, 37, 38
39, 40, 41

44, 45, 46
47, 48, 49

1,2,3
4,5,6
7,8,9
10,11,12
13,14,15
16,17,18
19,20,21,
22,23,24,
25,26,27,
28,29,30,
31,32,33,
34,35,36,
37,38,39,
40,41,42,
46,47,48,
49,50,51,
52,53,54,
55,56,57,
58,59,60,

---

1, 2, 3
5, 6, 7
8, 9, 10
12, 13, 14
15, 16, 17
21, 22, 23
24, 25, 26
28, 29, 30
31, 32, 33
36, 37, 38
39, 40, 41
44, 45, 46
47, 48, 49
51, 52, 53
53, 54, 55
57, 58, 59

For reporters

For reporters, prepare each PSD file as described above. Run spotifier.py for each plate to check if everything is correct:

python spotifier.py testdata/repoters/2.txt testdata/repoters/1.psd

and then run this cmd to process each PSD files and combine all outputs into one figure.

python spotifier.py testdata/repoters/2.txt testdata/repoters/*.psd

Digitifier

Process a figure into numbers:

  python digitifier.py 8 6 testdata/digitfier/1_all.png
[  3.         238.12373299 434.86099169 -27.59790191  96.14306032
 289.4862576  391.415654   242.01505869]
          0
0  0.066164
1  0.574584
2  1.000000
3  0.000000
4  0.267572
5  0.685648
6  0.906056
7  0.582999
Output created testdata/digitfier/1_all_plot.png

Install

To download the tool and install it run (with this you will get all test files):

pip install -e git+http://github.com/mmagnus/yeast-spotifier.git#egg=yeast-spotifier

if you want to have only the code installed in your system, simply run:

pip install yeast-spotifier

Changelog

1.1.

• --dont-align -> --align (align is worse right now hmm... so the default is --dont-align)
• use -1 in mapping to put a white box, you can use to make spacers for your figures

Mapping: 1,-1,2

1.1 initial code