# mo-lu-20170405-1a

## Detailed Information

  * Structure, deposition
  * B6C3F1, female
  * 10 min exposure, 1 micron red aerosol
  * Airways filled with clear OCT. Embedded in 0.75% black OCT.
  * Trachea sliced first. Heart in place.
  * 4 fiducial markers
    * Fluorescein 1 drop/70mL OCT
    * Alexa Fluor 633 16uL stock/mL OCT
  * D7100, 200mm lens, f/16
  * 72x222mm lens to enhance PE300
  * Focus x=UVND2, m=535/30

## Imaging Protocol

  * Lamp on 14:15
  * Scale:
    * dx = 4.64 microns
    * dy = 4.64 microns
    * dz = 9.52 microns
  * Approx image orientation: LAS

|            | Setting |   mt   |   ol   |   fl   |   rd   |       Notes           |
|-----------:|:-------:|:------:|:------:|:------:|:------:|:----------------------|
|            |    x    | UVND2  | UVND2  | 485/20 | 560/20 |                       |
|            |    m    | n/a    |470/30  | 535/30 | 635/30 |                       |
|            |    n    |        | 1      | 1      | 1      |                       |
|            |    f    |        | 0      | 0      | 400    |                       |
|            |    i    |        | 1      | 1      | 1      |                       |
|            |    h    |        | F      | F      | T      |                       |
| **Time**   |**Image**|**E/G** |**E/G** |**E/G** |**E/G** |    **Notes**          |
|15:34       |white-01 |25/160  |125/160 |6s/160  |167/160 |(53.5->57.6) 4.1mm rhodamine b 1 drop/10mL OCT |
|15:51       |cal      |20/160  |50/160  |40/160  |200/160 |PE beads. x=UVND2      |
|16:01       |white-11 |25/160  |125/160 |50/160  |333/160 |white paper, foil-backed, x=UVND2 |
|16:01       |white-12 |25/160  |25/160  |2/160   |2/160   |white paper, foil-backed, m=EMPTY |
|16:40       |1        |        |50/160  |15s/160 |333/160 |45mm. 43sec/slice                 |
|+00:44      |661      |        |        |        |        |Died at fl acquire. Lamp off +01:44 |
|+11:38      |661      |        |        |        |        |Lamp on +11:15. Sample wiped with moist Kimwipe. |
|+11:42      |664      |        |        |        |        |Increasingly blurry. Stopped. Re-focused.        |
|++01:44     |1803     |        |        |        |        |Done. 28mm.            |
|++01:43     |dark     |        |        |        |        |Darks taken. Lamp off. |

## Slicing Notes

  * Lamp off ++01:42 (delta=25.6h) TOTAL=260.8h
  * Sample broke before embedding, breaking off part of the trachea.
    * The tracheal wall is missing at the top of the sample
    * The remaining trachea is very short
  * The sample fell inside the liquid embedding material when I was
    trying to freeze it.
    * The sample may have fallen into an unknown orientation
    * The lung fell all the way to the bottom of the sample
  * Two top fiducial markers were missing before slicing was
    finished. One of the tubes might have been pulled out.
  * Still not sure why the blur increases after catching acquisition
    error (see slices 661-664).