Progress notes 24th and 25th of July

[lilysandstrom]

• [x] Turned all images from "keep" folders to the optimal orientation for processing

• [x] Sorted all images into folders according to orientation of scalebar for all four species. Subfolder names are in the following pattern: "M.intermedia-scalebar-left", located within their respective species folders (eg. ~/Desktop/microporella-subset-jpg/M_intermedia/M.intermedia-scalebar-left).

• [x] Finished lists of all images where other species are present (and detected by DeepBryo), for M. discors, M. agonistes and M. speculum. These are named "Speculum_images_with_other_species.csv" etc, located in ~/Documents/GitHub/bryozoa/microporella/Data. In each file, column 1 is image_id. Column two is blank when image has another bryozoa species detected by DeepBryo. If the presence of other bryozoa species were not immediately obvious to the viewer I have used column two to note their position, eg. "Other species upper left". I also used column two to note images with cracks that affect measurements, or when DeepBryo detects non-bryozoa taxa as zooids with features.

• [x] Started list of images with other species present for M. intermedia. Finished images in "M.intermedia-scalebar-left"

To do:

• [x] Finished list of all M. intermedia images with other species present.

• [x] CLI-csv files are still present in the M.intermedia subfolders, and should be deleted or moved

• [x] Manually done csvs moved to their correct place on GitHub (~/Documents/GitHub/bryozoa/microporella/Data/Manual-outputs/M.intermedia)

• [x] Redo high throughput with ext version of CLI

[lilysandstrom]

• [ ] Make four csvs with image_id and object_ids to remove, for each of the following lists of all images where other species are present manually:
• [ ] Speculum_images_with_other_species.csv
• [ ] intermedia_images_with_other_species.csv
• [ ] Agonistes_images_with_other_species.csv
• [ ] Discors_images_with_other_species.csv

[lilysandstrom]

• [ ] Go through omit folders, add image_id to the lists titled Speciesname_images_with_other_species.csv, and move images to correct "keep" folder (by optimal scalebar orientation):
• [x] omit_intermedia
• [ ] omit_speculum
• [ ] omit_agonistes
• [x] omit_discors Useable images from omit folders without other species are moved directly into their respective "keep" folder without notes