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anaphase_counts.md

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Anaphase counts

  • Go to example_folder/8_anaprog/ and make a new folder selections, and inside this folder:

  • Make a copy of the zt-MIP into example_folder/8_anaprog/ and rename *_anatet.tif.

  • Open *_anatet.tif in ImageJ/FIJI and set scale 512 to 833 (or 1996, see ori info).

  • Use free select to make a circle around each anaphase cell.

  • Save the xy coordinates for each cell in the anasel folder.

    • Use #-i.txt name for an anaphase I cell
    • Use #-ii.txt name for an anaphase II cell.
    • # is number of anaphase cells counted in field.

  • Open the selection combiner, change directory, and run.

  • Go to example_folder/4_dist_out/ and open the *_viewpost.png image in ImageJ/FIJI.

  • Set the origins depending on image size (see ori info).

  • Click on each number with the multi-point tool.

  • Press Cmd+m to gete measurements.

  • Go to to example_folder/3_cellobs/, open observation spreadshet and paste the xy positions into num, X, and Y, columns, then save the spreadsheet as *_xy.xlsx.

  • Copy the *_xy.xlsx spreadsheet into the example_folder/8_anaprog/selections folder.

  • Copy the mipjpg script to example_folder/2_vid_mip/2_vid/.

  • Open the Stack.tif in ImageJ/FIJI, auto adjust brightness and contrast, and save as Stackbc.tif.

  • Open mipjpg.txt, change directory, and copy commands into terminal.

  • Change file numbering to use leading zeros (01-09).

  • Copy jmip folder to example_folder/8_anaprog/selections/.

  • Open the anaphase cell position video script and change directory.

  • Change xy file name and run.

  • Open the animate script, change directory, and run in terminal.