4. “Slice n,” on column C, is time information. View5D assigns
0 (t 0 ) to the first tracking time point, while Manual Tracking
assigns 1 (t 1 ). Hence, copy column “Time [time]” from the
View5D file (either column G or N) plus one (1) into
column C.
5. Under “X” and “Y,” on columns D and E, copy the information corresponding to the X and Y coordinates in pixels (“PosX
[pixels]” and “PosY [pixels],” in the View5D file).
6. To add a second cell, go to the row below the last row
corresponding to this cell, and perform steps 3–5, adding a
two (2) in column B (or the next number track in View5D).
7. Repeat this process for all cells of interest, adding 3, 4, 5, etc. as
their corresponding value on column B.
8. Once you have added all the tracks that you wish to visualise,
add a correlative number list (1, 2, 3. . .) on column A, starting
on cell A2 and continuing until the last time point of the
last cell.
9. Save this file as file type “Text (Tab delimited).”
For automatic conversion, follow steps 10–16:
10. Open the tracking file from the View5D output on Microsoft
Excel.
11. Save this file as file type “Excel 97-2003 Workbook.”
12. Open MatLab.
13. Copy the script in the file “transform_to_manual_track.txt”
(Supplementary Script 2) onto a new workbook.
14. Run the script by pressing the green arrow button on the top
ribbon.
15. Find the Excel file that you saved on step 2.
16. A window called “Data Specification” will pop up that requires
information on the Excel file. The first space is the name of the
Tab containing the tracking data. The second space is the total
number of time points. The third one is the total number of
rows containing information (it will be the number of the row
immediately above the row with “#Statistics Summary,” at the
bottom of the file). Press OK. This will create a file on the same
directory that has your Excel file, called “name.xls_markers_ManualTrack.txt.”
Once you have the text file, upload it to Manual Tracking.
17. Open the 3D movie in Fiji.
18. Create a 2D maximal projection (“Image > Stack > Z
project. . .” a window will open to select the type of projection.
Select Max Intensity, or the preferable mode of projection and
click “OK”).
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0 (t 0 ) to the first tracking time point, while Manual Tracking
assigns 1 (t 1 ). Hence, copy column “Time [time]” from the
View5D file (either column G or N) plus one (1) into
column C.
5. Under “X” and “Y,” on columns D and E, copy the information corresponding to the X and Y coordinates in pixels (“PosX
[pixels]” and “PosY [pixels],” in the View5D file).
6. To add a second cell, go to the row below the last row
corresponding to this cell, and perform steps 3–5, adding a
two (2) in column B (or the next number track in View5D).
7. Repeat this process for all cells of interest, adding 3, 4, 5, etc. as
their corresponding value on column B.
8. Once you have added all the tracks that you wish to visualise,
add a correlative number list (1, 2, 3. . .) on column A, starting
on cell A2 and continuing until the last time point of the
last cell.
9. Save this file as file type “Text (Tab delimited).”
For automatic conversion, follow steps 10–16:
10. Open the tracking file from the View5D output on Microsoft
Excel.
11. Save this file as file type “Excel 97-2003 Workbook.”
12. Open MatLab.
13. Copy the script in the file “transform_to_manual_track.txt”
(Supplementary Script 2) onto a new workbook.
14. Run the script by pressing the green arrow button on the top
ribbon.
15. Find the Excel file that you saved on step 2.
16. A window called “Data Specification” will pop up that requires
information on the Excel file. The first space is the name of the
Tab containing the tracking data. The second space is the total
number of time points. The third one is the total number of
rows containing information (it will be the number of the row
immediately above the row with “#Statistics Summary,” at the
bottom of the file). Press OK. This will create a file on the same
directory that has your Excel file, called “name.xls_markers_ManualTrack.txt.”
Once you have the text file, upload it to Manual Tracking.
17. Open the 3D movie in Fiji.
18. Create a 2D maximal projection (“Image > Stack > Z
project. . .” a window will open to select the type of projection.
Select Max Intensity, or the preferable mode of projection and
click “OK”).
Tools to Study Neural Crest Migration in Zebrafish
99