Optima Plate Reader
Optima Plate Reader kdorfman Tue, 01/17/2017 - 19:12Link 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 - 15:20Look 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
-
Lab 3.1 (2022) counting bacteria: std curve OD vs population density ↩︎
-
Lab 4.2 (2022) lac operon shake cells, then read OD for overnight growth curves – part of script “Grow&Glow” ↩︎
-
Lab 4.2 (2022) lac operon after BugOD Shake,read FL for overnight growth curves– part of script “Grow&Glow” ↩︎
-
Lab 1.3 serial dilution; absorbance of fluorescein; std curve ↩︎
-
Lab 1.3 serial dilution; fluorescence of fluorescein; std curve ↩︎
Script for lac operon lab
Script for lac operon lab kdorfman Mon, 10/24/2022 - 15:18Script 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)