Meeting focus was on section naming conventions. Decision is for Hannah and Litao to devise a scheme that can be put into DataTable and also be used to order tiffs outside of the pipeline (i.e. conversions AND naming to be done outside of pipeline)
Where we are at: Here is a recent Bioformat based conversion on Jan 2 - It gave ascending order for sections (but not sequential and placeholders not noted):
DK37_slide003_2019_11_25_S1_C0_CFP-raw.tif
DK37_slide003_2019_11_25_S7_C0_CFP-raw.tif
DK37_slide003_2019_11_25_S12_C0_CFP-raw.tif
DK37_slide003_2019_11_25_S17_C0_CFP-raw.tif
DK37_slide004_2019_11_25_S1_C0_CFP-raw.tif
DK37_slide004_2019_11_25_S7_C0_CFP-raw.tif
DK37_slide004_2019_11_25_S13_C0_CFP-raw.tif
DK37_slide004_2019_11_25_S19_C0_CFP-raw.tif
Hannah met with Litao to explain more about czis and text files.
Litao will work on table to input:
- the file pathways (birdstore locations of czis)
- the czi names from scanner
- the metadata (date of scan etc that comes from scanner)- note these names will need further modification to be useful for conversion workflow
4.in parallel the Hannah- generated- textfile will be put into the table or a file path to where it is located will be documented
Still open issue is consensus between Alex, Sid, Litao and Hannah on how to name file so that converter output includes unambiguous id of each good section, each problematic or missing section
And plan is for this to be done outside of the pipeline so that if correction can be made (eg swap in rescanned blurred section image) prior to pipeline entry
Meeting focus was on section naming conventions. Decision is for Hannah and Litao to devise a scheme that can be put into DataTable and also be used to order tiffs outside of the pipeline (i.e. conversions AND naming to be done outside of pipeline)
Where we are at: Here is a recent Bioformat based conversion on Jan 2 - It gave ascending order for sections (but not sequential and placeholders not noted):
DK37_slide003_2019_11_25_S1_C0_CFP-raw.tif
DK37_slide003_2019_11_25_S7_C0_CFP-raw.tif
DK37_slide003_2019_11_25_S12_C0_CFP-raw.tif
DK37_slide003_2019_11_25_S17_C0_CFP-raw.tif
DK37_slide004_2019_11_25_S1_C0_CFP-raw.tif
DK37_slide004_2019_11_25_S7_C0_CFP-raw.tif
DK37_slide004_2019_11_25_S13_C0_CFP-raw.tif
DK37_slide004_2019_11_25_S19_C0_CFP-raw.tif
Hannah met with Litao to explain more about czis and text files.
Litao will work on table to input:
4.in parallel the Hannah- generated- textfile will be put into the table or a file path to where it is located will be documented
Still open issue is consensus between Alex, Sid, Litao and Hannah on how to name file so that converter output includes unambiguous id of each good section, each problematic or missing section
And plan is for this to be done outside of the pipeline so that if correction can be made (eg swap in rescanned blurred section image) prior to pipeline entry