From f5906f74e1601140ecb893a3d2b6664bf1bc98fe Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Mon, 18 Aug 2025 13:53:37 -0400 Subject: [PATCH] Add 1PE to complement 2PE https://blog.biodock.ai/one-vs-two-photon-microscopy/ seems to provide a nice comparison between one- and two-photon microscopy. Also https://www.gophotonics.com/community/what-are-single-photon-and-two-photon-excitation provides another comparison and uses "excitation" consistently between them. Note that there is also already "FLUO" suffix for "Fluorescence microscopy" in general, of which both 1PE and 2PE and likely MPE (multi-photon) mechanisms are, so unclear when FLUO to be used, but I guess 2PE, MPE and now 1PE should be RECOMMENDED to be used in favor of FLUO as more specific --- src/modality-specific-files/microscopy.md | 3 ++- src/schema/objects/suffixes.yaml | 5 +++++ src/schema/rules/files/raw/micr.yaml | 1 + 3 files changed, 8 insertions(+), 1 deletion(-) diff --git a/src/modality-specific-files/microscopy.md b/src/modality-specific-files/microscopy.md index 617407cd0c..e27f862049 100644 --- a/src/modality-specific-files/microscopy.md +++ b/src/modality-specific-files/microscopy.md @@ -28,7 +28,7 @@ and a guide for using macros can be found at https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md --> {{ MACROS___make_filename_template("raw", datatypes=["micr"], suffixes=["TEM", "SEM", "uCT", "BF", "DF", -"PC", "DIC", "FLUO", "CONF", "PLI", "CARS", "2PE", "MPE", "SR", "NLO", "OCT", "SPIM", "XPCT"], n_dupes_to_combine=4) }} +"PC", "DIC", "FLUO", "CONF", "PLI", "CARS", "1PE", "2PE", "MPE", "SR", "NLO", "OCT", "SPIM", "XPCT"], n_dupes_to_combine=4) }} Microscopy data MUST be stored in the `micr` directory. @@ -82,6 +82,7 @@ and a guide for using macros can be found at "CONF", "PLI", "CARS", + "1PE", "2PE", "MPE", "SR", diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml index 1e2825ced2..2d54d9a1e4 100644 --- a/src/schema/objects/suffixes.yaml +++ b/src/schema/objects/suffixes.yaml @@ -1,6 +1,11 @@ --- # This file defines valid BIDS file suffixes. # For rules regarding how suffixes relate to datatypes, see files in `rules/files/raw/`. +OnePE: + value: 1PE + display_name: 1-photon excitation microscopy + description: | + 1-photon excitation microscopy imaging data TwoPE: value: 2PE display_name: 2-photon excitation microscopy diff --git a/src/schema/rules/files/raw/micr.yaml b/src/schema/rules/files/raw/micr.yaml index b256033ce9..8621219ad6 100644 --- a/src/schema/rules/files/raw/micr.yaml +++ b/src/schema/rules/files/raw/micr.yaml @@ -12,6 +12,7 @@ microscopy: - CONF - PLI - CARS + - 1PE - 2PE - MPE - SR