Optima Plate Reader

Optima Plate Reader kdorfman Tue, 01/17/2017 - 19:12

Link to Programs here

sign in to the "student" account
user = .\student pw = student@ISB364

Find Optima Control in the start menu

Folders icon pinned to taskbar

Data files go to: This PC > Local Disc (C:) > users > student > documents
(also to backups)

Find protocols to import in: This PC > Local Disc (C:) > users > Public > Public Downloads > PS1_Protocols

Plate IDs (in the run menu)
ID1 is file name. Be sure to give a file name

To get the meta data on the output csv file:
Setup
Program configuration
preferences
define format

Set Preferences before running a script! See p 28 of user manual ii, below.

Setup > Program Configuration > Define Format > Filename and Path

File info

Overwrite, append, make new file with same name + number

Header:

  • no header - just the data - useful for files that have to be compiled
  • long header includes wavelength - just the right amount of info (USE THIS)
  • full header (Ex, Em wavelength, date, time, etc) way too much info
  • short header does not include wavelength
  • Danish headers writes the file name next to the row ID. (!?!)

Style

  • Table: no well numbers, or wavelength indicators, etc. Just the results in plate layout form.
  • Table with well numbers: puts the well IDs next to the reading (Very hard to read)
  • Table with well numbers (only measured wells)
  • Table with well numbers in plate layout style: USE THIS

  • List (Literally, a list. no plate info. all values in one column)

  • List with well numbers

    A B
    1 A01 10
    2 A02 12
    3 A03 11
    4 A04 13
  • List with well numbers (only measured wells): puts a - for a skipped well)

  • List sorted by wells (all cycles in one row, chromatics in separate blocks)
  • List sorted by wells with well numbers
  • List sorted by well numbers (only measured wells)
  • List sorted by wells (all cycles/intervals/channels/chromatics in one row)
  • List sorted by wells 2 " " " (only measured wells)

Script mode

For i = 1 to 72 This is the counter
id 1 = "BOD1" BOD1 is the file name
id 1 = "BOD1" i makes a separate file for each run, called BOD1_1. BOD1_2 etc.

Excitation filters Emission filters
340 520
485 570
492 590
530 620
544
584
595

Plate Reader Programs

Plate Reader Programs kdorfman Thu, 10/13/2022 - 15:20

Look for Programs here

Desktop/This PC/Local Disc (C:)/Users/Public/Public Downloads/PS1_Protocols

or

On Pstar2, even though the files say Polar star 1):

Desktop/This PC/Local Disc (C:)/Users/Public/Public Downloads/polarstar1/PS1_Protocols

Program Layout method ex em vol
BUG OD 1 A&B Abs 595 . 250
BUG_FLUOR 2 A:H FL 486 520 .
BUG_OD_SHAKE 3 A:H ABS 595 . 200
FL-ABS-BY-2 4 C1:2, D ABS 485 . 150
REPEATABILITY 5 A & B ABS 485 . 150
SERIAL2&5_ABS 6 E1-5, F:H ABS 485 . 150
SERIAL2&5_FL 7 E1-5, F:H FL 485 520 .
REPEATAILITY_FL 8 A:B FL 485 520 .

Script for overnight growth and fluorescence


  1. Lab 3.1 (2022) counting bacteria: std curve OD vs population density ↩︎

  2. Lab 4.2 (2022) lac operon shake cells, then read OD for overnight growth curves – part of script “Grow&Glow” ↩︎

  3. Lab 4.2 (2022) lac operon after BugOD Shake,read FL for overnight growth curves– part of script “Grow&Glow” ↩︎

  4. Lab 1.2 serial dilution & plate reader sensitivity ↩︎

  5. Lab 1.2 pipetting consistency (ABS) ↩︎

  6. Lab 1.3 serial dilution; absorbance of fluorescein; std curve ↩︎

  7. Lab 1.3 serial dilution; fluorescence of fluorescein; std curve ↩︎

  8. (Lab 1.2) pipetting consistency (FL) not used in 2022 ↩︎

Script for lac operon lab

Script for lac operon lab kdorfman Mon, 10/24/2022 - 15:18

Script for overnight growth and fluorescence

Set Preferences inside the user dialog box before running a script!

Location: C:\Users\Public\Downloads\PS1_Protocols\E_Coli_Grow&Glow.btc

(or PS2)

Multiple measurements for 17.5 hours

;absorbance and fluorescence

st1:="BUG_OD_SHAKE"

st2:="BUG_FLUOR"

for i:=1 to 70 do begin

ID1:="BOD1"

ID2:= <protocol>

ID3:=<method>

R_Run "<st1>"

ID1:="BFL1"

ID2:= <protocol>

ID3:= <method>

R_Run "<st2>"

wait for 13 m

end;

beep

(Names for PS2 = BOD2, BFL2)