Kaitlyn’s notebook: Uploading histology photos

Today and yesterday I worked on removing photos from my phone that I took of Laura’s histology and renaming the files with their appropriate sample numbers. This required using the orientation off the casette and matching it to the block. It looks like the casettes were mirrored on the slides but stayed consistent throughout all slides.

Once all the samples were matched to the appropriate tissue on the slide, I began renaming files according to the histology data management plan. File labels are DATE-SAMPLE-MAGNIFICATION (eg. 20180730-270-4X). I created a new folder in owl for O. lurida in /web/hesperornis to upload the photos.

I realized that the sample ID’s were not going to be helpful if someone wanted to find the slide and re-image or analyze it. Therefore, I created a new folder containing the date and slide labels (eg. 20180730-OLY82-107). This will allow someone to find the images based off of the slides or help someone know what slides contain these samples. I’m not sure if this will be a convention we will want to keep in the Roberts lab, but I thought that adding the slide number into the file label would create too lengthy of a name. One more benefit the new folder added is that the “maps” I created that showed which samples are on each slide can be kept separate from other slide images/experiments. However, it could just as easily be parsed out based on the date.

There was one problem labeling the histology slides. Slide OLY 102 had 7 tissue samples on it, however the casette shows that only 6 tissues were placed. Samples 355 and 353 are indistinguishable thus they are labeled “..355-353A..”, “..355-353B..”, and “..355-353C..”. Additionally, some slides had some hair caught in them. I imaged OLY 96, sample 317 and added “hair” into the label. All images are viewable here

I also downloaded ImageJ onto Emu yesterday. I tried to add it to Ostrich, but the srlab user is not an admin which is required for download.