From 0b7228c06c4fae8554507548782e489ef7e9c604 Mon Sep 17 00:00:00 2001
From: Erin Weisbart <54687786+ErinWeisbart@users.noreply.github.com>
Date: Mon, 10 Apr 2023 13:10:06 -0700
Subject: [PATCH] mat => npy in appendix file structure

we now make illum correction as .npy not .mat files
---
 06-appendix.md | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/06-appendix.md b/06-appendix.md
index a4426fb..cfd16ad 100644
--- a/06-appendix.md
+++ b/06-appendix.md
@@ -17,7 +17,7 @@ this handbook
         image data
     -   The `illum` folder is identical to the `images` folder in terms
         of structure
-        -   `illum` is an output of the first stage of cell profiler
+        -   `illum` is an output of the first stage of CellProfiler
             pipeline that stores a function to adjust the plates in
             `images`
 -   `workspace` also has subdirectories
@@ -87,12 +87,11 @@ this handbook
     ├── 2016_04_01_a549_48hr_batch1
     │   ├── illum
     │   │   └── SQ00015167
-    │   │       ├── SQ00015167_IllumAGP.mat
-    │   │       ├── SQ00015167_IllumDNA.mat
-    │   │       ├── SQ00015167_IllumER.mat
-    │   │       ├── SQ00015167_IllumMito.mat
-    │   │       ├── SQ00015167_IllumRNA.mat
-    │   │       └── SQ00015167.stderr
+    │   │       ├── SQ00015167_IllumAGP.npy
+    │   │       ├── SQ00015167_IllumDNA.npy
+    │   │       ├── SQ00015167_IllumER.npy
+    │   │       ├── SQ00015167_IllumMito.npy
+    │   │       └── SQ00015167_IllumRNA.npy
     │   └── images
     │       └── SQ00015167__2016-04-21T03_34_00-Measurement1
     │         ├── Assaylayout