tCountdown for all hands meeting on 12 Feb

[david-kleinfeld]

Preprocessing Transform raw data into ordered, inspected, aligned and normalized data in TIFF format.
• DK 37 and DK 39 all files CZI and TIFF on Birdstore
• Encompasses steps (1 to 5 from Alex Notes) of prior Preprocessing, so that final tiffs are section-to-section oriented to a standard view and aligned and the intensity of the counterstain channel is normalized.
• Final files are ready for conversion for viewing on NeuroGlancer (Ed and Sidd)

Completing the pipeline:
• DK 37 (Basalis) - This had Ch 1 only - fully converted to TIFF.
• DK 39 (Ratto) - This has 3 channels - only 75 % converts
To be section to section aligned, normalized.
Covert into pyramid format tiles for NeuroGlancer
Check with Beth for visual inspection with NeuroGlancer

Intermediate re-evaluation by Wed 5 Feb.

Fixing Problems.
• Reference to DK 39 - This has 3 channels - only 75 % of slides convert
Understood nature of CZI to TIFF failures. Potential systematics:
Were these rescan files (side 100)?
Local versus cloud conversion?
Need to understand nature of 5X-smaller files under rescan

[yoavfreund]

Below is a checklist for processing a brain:

1. Convert CZI to Tiff
2. create sections table with placeholders
3. Align sections
   3.1 Generate translation/rotation matices.
   3.2 Rotate images.
4. (Optional) Normalize gray values
5. Prepare tiles for neuroglancer
6. Run neuroglancer to view brain.

There are two brains we are preparing for Feb 12: DK37 (one channel) , DK39 (3 channels)

Please create a list of 6 items for each brain, and for each item state:
Complete without errors
Partially complete

Leave empty if neither.

[CodingDonky]

Status of DK37 (ongoing):

1. [DONE] Convert CZI to Tiff
2. [DONE] create sections table with placeholders
3. Align sections DONE
4. (Optional) Normalize gray values DONE
5. Prepare tiles for neuroglancer DONE
6. Run neuroglancer to view brain redoing on old tech stack

Status of DK39 (ongoing):

1. [DONE] Convert CZI to Tiff
2. [DONE] create sections table with placeholders
3. [DONE - Done by the night of Feb 5th] Align sections
   3' An almost perfect alignment is ready. Available on Birdstore at:
4. (Optional) Normalize gray values
5. Prepare tiles for neuroglancer. This is done for 1st channel @sidd and @ed are working on this.
6. Run neuroglancer to view brain