Koehler illumination and DIC configuration for inverted and upright microscopes

All HCBI coverslip corrected objectives are corrected for #1.5 Coverslips. Please ensure you are ONLY using #1.5 slips.

Click here for the HCBI's recommendations for mounting media.  See also this great document from UCSF.


Lightsheet consumables(HCBI recommended suppliers)
Guide to Lightsheet sample prep (Zeiss)
Click here to view a video of Lightsheet sample prep (Zeiss)
Guide to stitching tiles with Arivis software

Tissue Clearing

Clearing with CLARITY and the X-CLARITY ETC system
Immunostaining for cleared tissue (from Renier et al., Cell, 2016)

Axio Scan

Axio Scan Application Guide

PALM Laser Microdissection

Immunohistochemistry on frozen sections prior to microdissection and RNA extraction
Sample staining, mounting, and cutting for RNA extraction
Quickguide to PALM microdissection consumables
RNA extraction from formalin fixed paraffin embedded (FFPE) sections
RNA extraction from frozen sectionsImmunofluorescence on frozen sections


Multi-color channel alignment 
PALM/STORM sample prep

LSM 780/880

Guide to FCS experiments


Tiling and focusing with ZEN Blue




lightsheet_consumables.pdf192 KB
lightsheetz1_sample-preparation_zeiss.pdf1.25 MB
ihc_and_rna.pdf18 KB
palm_consumables_quickguide_2012_rev_d.docx61 KB
zeiss_labprotocol_immunofluorescence_0310.pdf407 KB
zeiss_lcm_protocol_rna_ffpe_0212.pdf482 KB
zeiss_lcm_protocol_rna_frozen_0212.pdf161 KB
en_41_011_065_elyra_sample-prep-quickguide.pdf951 KB
elyra_sim_channel_alignment_protocol.pdf154 KB
guide_to_basic_fcs_experiment.pdf1.65 MB
zeiss_labprotocol_rna_0811.pdf4.91 MB
axio_scan.z1_application_guide.pdf5.18 MB
tile_imagingfocus_faq_rev_03-14.pdf1.19 MB
aim_zen2012_aim_dic_inverted_lsm.pdf491 KB
aim_zen2012_aim_dic_upright_lsm.pdf444 KB
en_quick-guide_lightsheet-z.1_arivis-stitching.pdf3.12 MB
hcbi_clarity_protocol.pdf110 KB
immunostaining_protocol.pdf826 KB