Package: yeast-spotifier
SpotifierThis 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 plateshttps://github.com/mmagnus/yeast-spotifier/releases/download/v1.0/templates-for-copper-plates.zip!Table of ContentsSpotifierOptionsPrepare imageAdjust the image to the templatePrepare mapping fileCustomizationMappingsFor reportersDigitifierInstallChangelogCreated bygh-md-tocOptionsusage: 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-annotateFig.-t,  trim background to get nicely formatted dots.Prepare imageOpen the image:Image -> Adjustments -> Black & white OR cmd+alt+shift+bInverse 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 templateOpen template.psd and drag and drop plate photoLower 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 fileOpen 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.txtThe results should be like this:and the files02_30_spots.pngshould be created in the folder next to the input file (in this casetestdata/s02/s02_30_spots.png)TIP: If you want to introduce one extra, empty line, just add an empty line to a map file.CustomizationIf 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.txtUse play with Opacity to see Backgound with the template to adjust positions of your dosts.MappingsSome 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, 59For reportersFor 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.psdand 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/*.psdDigitifierProcess 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.pngInstallTo 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-spotifierif you want to have only the code installed in your system, simply run:pip install yeast-spotifierChangelog1.1.--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 figuresMapping: 1,-1,21.1 initial code