I am Edouard, PhD student in plant biology. I am actually doing a lot of confocal imagin on an LSM880 controlled with Zen Black 2.1 (i guess).
I am following a standard procedure that I have been developping for a year now. During this procedure, I had to do a tile scan that I use for localize nuclei on a whole tissue sample (tomato pericarp). When I finished to localize nuclei of interests I then save the windows view in tif, this allows me to find back the position (later during the image analysis step) of each individual nuclei that I acquired independantly using a higher resulation.
I encountered a problem on a sample because I forgot to save the window view of the tile scan with the tagged nuclei (image with crosshair). So, I tried to re-open my tile scan and the position file into ZenBlack but I did not succed to get back the view of the crosshair on the image.
Do you know, how I can do it ?
or even use this position file to easily find back nuclei on the picture on image j ?
I join a resume of how I proceed :
1- Tile scan of my sample with x63 objectives (generally 3x4 tiles with 30z of 1.5µm)
2- Stiching of the tile scan and localization of nuclei with position tool (generally 40-60 nuclei)
3- Classification of nuclei by depth to group acquisition of nuclei by size and depth in experiment designers
4- Some hours of acquisition
5- Image analysis
FisH spot quantification
nuclei volume measurement
mapping of nuclei into the whole tile using the window view (join file, hoping that you can see)
cell size measurement
nuclei volume measurement
mapping of nuclei into the whole tile using the window view (join file, hoping that you can see)
cell size measurement
Edouard, PhD student in Plant biology, Bordeaux University